Course Information

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
In-person direct teaching

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)
Mgr. Adéla Finstrlová, Ph.D. (assistant)
Mgr. Ivana Mašlaňová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 12 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology and bioinformatics. DNA and protein sequence databases. Primary and secondary databases. Unique identifiers. Keyword and sequences searches, advantages and disadvantages. Scores and E-values.
• DNA sequencing techniques.Types of sequencing libraries. Automatic Sanger sequencing. Next Generation Sequencing (NGS). Third generation sequencing. Approaches for sequence assembly.
• Manipulation with sequence data, primer design. Sequence format conversions, in silico translation. Searching for motifs, restriction sites, computational analysis. Design of primers.
• Tools and algorithms for local sequence alignment. Algorithms and software tools for multiple sequence alignment. Global and local alignments. Fast versus accurate algorithms. Conserved motif search. Databases of motives and their use in biology research.
• Computational gene identification. Comparative genomics. Tools and algorithms for automatic annotation of genomic sequences. NGS data analysis and local annotation. Submitting the genomic sequence to the primary database.
• Protein structure databases. Primary and classification databases. Methods to determine protein structure with atomistic resolution. Prediction of protein structure.
• Phylogenetic analysis based on nucleotide and protein sequences. Phylogenetic trees, their biological interpretation and use in biological research. Ancestral proteins and their properties.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi5000c Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

https://loschmidt.chemi.muni.cz/bioinf/

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)
Mgr. Adéla Finstrlová, Ph.D. (assistant)
Mgr. Ivana Mašlaňová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 12 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology and bioinformatics. DNA and protein sequence databases. Primary and secondary databases. Unique identifiers. Keyword and sequences searches, advantages and disadvantages. Scores and E-values.
• DNA sequencing techniques.Types of sequencing libraries. Automatic Sanger sequencing. Next Generation Sequencing (NGS). Third generation sequencing. Approaches for sequence assembly.
• Manipulation with sequence data, primer design. Sequence format conversions, in silico translation. Searching for motifs, restriction sites, computational analysis. Design of primers.
• Tools and algorithms for local sequence alignment. Algorithms and software tools for multiple sequence alignment. Global and local alignments. Fast versus accurate algorithms. Conserved motif search. Databases of motives and their use in biology research.
• Computational gene identification. Comparative genomics. Tools and algorithms for automatic annotation of genomic sequences. NGS data analysis and local annotation. Submitting the genomic sequence to the primary database.
• Protein structure databases. Primary and classification databases. Methods to determine protein structure with atomistic resolution. Prediction of protein structure.
• Phylogenetic analysis based on nucleotide and protein sequences. Phylogenetic trees, their biological interpretation and use in biological research. Ancestral proteins and their properties.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi5000c Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

https://loschmidt.chemi.muni.cz/bioinf/

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)
Mgr. Adéla Finstrlová, Ph.D. (assistant)
Mgr. Ivana Mašlaňová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 12 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology and bioinformatics. DNA and protein sequence databases. Primary and secondary databases. Unique identifiers. Keyword and sequences searches, advantages and disadvantages. Scores and E-values.
• DNA sequencing techniques.Types of sequencing libraries. Automatic Sanger sequencing. Next Generation Sequencing (NGS). Third generation sequencing. Approaches for sequence assembly.
• Manipulation with sequence data, primer design. Sequence format conversions, in silico translation. Searching for motifs, restriction sites, computational analysis. Design of primers.
• Tools and algorithms for local sequence alignment. Algorithms and software tools for multiple sequence alignment. Global and local alignments. Fast versus accurate algorithms. Conserved motif search. Databases of motives and their use in biology research.
• Computational gene identification. Comparative genomics. Tools and algorithms for automatic annotation of genomic sequences. NGS data analysis and local annotation. Submitting the genomic sequence to the primary database.
• Protein structure databases. Primary and classification databases. Methods to determine protein structure with atomistic resolution. Prediction of protein structure.
• Phylogenetic analysis based on nucleotide and protein sequences. Phylogenetic trees, their biological interpretation and use in biological research. Ancestral proteins and their properties.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi5000c Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

https://loschmidt.chemi.muni.cz/bioinf/

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)
Mgr. Adéla Finstrlová, Ph.D. (assistant)
Mgr. Ivana Mašlaňová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 12 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)
Mgr. Adéla Finstrlová, Ph.D. (assistant)
Mgr. Ivana Mašlaňová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 prace doma

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 11 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics

Extent and Intensity

2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).

Teacher(s)

prof. Mgr. Jiří Damborský, Dr. (lecturer)
prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

Bi4010 Essential molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 11 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Jan Dvorský, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 17. 9. to Fri 14. 12. Tue 11:00–12:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && (NOW( Bi9060 Bioinformatics II ) || SOUHLAS)
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 18. 9. to Fri 15. 12. Tue 11:00–12:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && (NOW( Bi9060 Bioinformatics II ) || SOUHLAS)
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Learning outcomes

At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 19. 9. to Sun 18. 12. Tue 11:00–12:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && (NOW( Bi9060 Bioinformatics II ) || SOUHLAS)
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && (NOW( Bi9060 Bioinformatics II ) || SOUHLAS)
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 11:00–12:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 16. 9. to Fri 6. 12. Tue 14:00–15:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understand principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able to manipulate nucleotide and protein sequences in silico, design primers, perform pair and multiple sequence comparisons and phylogenetic studies, annotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submitting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 15:00–16:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Thu 8:00–9:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

there are 9 fields of study the course is directly associated with, display

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Thu 8:00–8:50 B11/306

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

Study Materials
The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Tue 10:00–11:50 G2,02003

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Wed 8:00–9:50 BR3

• Timetable of Seminar Groups:

Bi5000/01: Wed 10:00–10:50 COMPBR, R. Pantůček
Bi5000/02: Wed 11:00–11:50 COMPBR, R. Pantůček
Bi5000/03: Tue 16:00–16:50 COMPBR, R. Pantůček
Bi5000/04: Tue 14:00–14:50 COMPBR, R. Pantůček
Bi5000/05: Tue 15:00–15:50 COMPBR, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• Viz webová stránka předmětu.
• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods

Weekly lectures and exercises, homeworks concerning each practical topic, practical exam on PC.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Thu 8:00–9:50 BR3

• Timetable of Seminar Groups:

Bi5000/01: Thu 13:00–13:50 COMPBR, R. Pantůček
Bi5000/02: Thu 10:00–10:50 COMPBR, R. Pantůček
Bi5000/03: Thu 11:00–11:50 COMPBR, R. Pantůček
Bi5000/04: Thu 12:00–12:50 COMPBR, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Informační služby v počítačových sítích - využití v molekulární biologii a genetice. Prohledávání citačních databází (PubMed, WOS). Sekvencování DNA, metody analýzy genomů. Manipulace se sekvenčními daty (převody formátů sekvencí, restrikční analýza, návrh primerů). Stanovení podobnosti sekvencí (dot-plot, BLAST, Fasta). Mnohonásobné porovnávání sekvencí (ClustalW). Hledání genů a funkčních oblastí (GeneMark, Glimmer). Analýza sekvencí proteinů, databáze konzervativních domén proteinů. Funkční genomika. Predikce sekundární struktury RNA. Specializované programy pro molekulární biologii. Analýza elektroforetických gelů (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Wed 8:00–9:50 BR2

• Timetable of Seminar Groups:

Bi5000/01: Wed 10:00–10:50 COMPBR, R. Pantůček
Bi5000/02: Wed 11:00–11:50 COMPBR, R. Pantůček
Bi5000/03: Wed 12:00–12:50 COMPBR, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Informační služby v počítačových sítích - využití v molekulární biologii a genetice. Prohledávání citačních databází (PubMed, WOS). Sekvencování DNA, metody analýzy genomů. Manipulace se sekvenčními daty (převody formátů sekvencí, restrikční analýza, návrh primerů). Stanovení podobnosti sekvencí (dot-plot, BLAST, Fasta). Mnohonásobné porovnávání sekvencí (ClustalW). Hledání genů a funkčních oblastí (GeneMark, Glimmer). Analýza sekvencí proteinů, databáze konzervativních domén proteinů. Funkční genomika. Predikce sekundární struktury RNA. Specializované programy pro molekulární biologii. Analýza elektroforetických gelů (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: graded credit. Other types of completion: z (credit).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Mon 11:00–12:50 B1,01004

• Timetable of Seminar Groups:

Bi5000/01: Mon 13:00–13:50 01018, K. Chroust, R. Pantůček
Bi5000/02: Mon 14:00–14:50 01018, K. Chroust, R. Pantůček
Bi5000/03: Mon 15:00–15:50 01018, K. Chroust, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Working with MS Windows. Word processors - MS Word. Spreadsheets - MS Excel. Statistical software (examples from general and quantitative genetics). Informational and fact-finding services in computer networks: applications in molecular biology and genetics (Current Contents, Medline). Database searching of nucleic acids and proteins (BLAST, Fasta). Sequence alignments (Blast, ClustalW). Gene finding (GeneMark, Glimmer). Functional genomics. Genome research (human genome, Drosophila, mouse, Saccharomyces, Arabidopsis). Specialized software for molecular biology. Sequence analysis (DNASIS). Analysis of electropherograms (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: graded credit. Other types of completion: z (credit).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (seminar tutor)
RNDr. Ing. Karel Chroust, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable

Wed 11:00–12:50 B1,01004

• Timetable of Seminar Groups:

Bi5000/01: Thu 16:00–16:50 01018, K. Chroust, R. Pantůček
Bi5000/02: Thu 17:00–17:50 01018, K. Chroust, R. Pantůček
Bi5000/03: Thu 18:00–18:50 01018, K. Chroust, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Working with MS Windows. Word processors - MS Word. Spreadsheets - MS Excel. Statistical software (examples from general and quantitative genetics). Informational and fact-finding services in computer networks: applications in molecular biology and genetics (Current Contents, Medline). Database searching of nucleic acids and proteins (BLAST, Fasta). Sequence alignments (Blast, ClustalW). Gene finding (GeneMark, Glimmer). Functional genomics. Genome research (human genome, Drosophila, mouse, Saccharomyces, Arabidopsis). Specialized software for molecular biology. Sequence analysis (DNASIS). Analysis of electropherograms (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: graded credit. Other types of completion: z (credit).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (seminar tutor)
RNDr. Ing. Karel Chroust, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable of Seminar Groups

Bi5000/01: No timetable has been entered into IS. K. Chroust, R. Pantůček
Bi5000/02: No timetable has been entered into IS. K. Chroust, R. Pantůček
Bi5000/03: No timetable has been entered into IS. K. Chroust, R. Pantůček
Bi5000/04: No timetable has been entered into IS. K. Chroust, R. Pantůček
Bi5000/05: No timetable has been entered into IS. K. Chroust, R. Pantůček

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Working with MS Windows. Word processors - MS Word. Spreadsheets - MS Excel. Statistical software (examples from general and quantitative genetics). Informational and fact-finding services in computer networks: applications in molecular biology and genetics (Current Contents, Medline). Database searching of nucleic acids and proteins (BLAST, Fasta). Sequence alignments (Blast, ClustalW). Gene finding (GeneMark, Glimmer). Functional genomics. Genome research (human genome, Drosophila, mouse, Saccharomyces, Arabidopsis). Specialized software for molecular biology. Sequence analysis (DNASIS). Analysis of electropherograms (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: graded credit. Other types of completion: z (credit).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (seminar tutor)
RNDr. Ing. Karel Chroust, Ph.D. (seminar tutor)
doc. RNDr. Vladislava Růžičková, CSc. (seminar tutor)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Timetable of Seminar Groups

Bi5000/01: No timetable has been entered into IS. K. Chroust, R. Pantůček, V. Růžičková
Bi5000/02: No timetable has been entered into IS. K. Chroust, R. Pantůček, V. Růžičková

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Working with MS Windows. Word processors - MS Word. Spreadsheets - MS Excel. Statistical software (examples from general and quantitative genetics). Informational and fact-finding services in computer networks: applications in molecular biology and genetics (Current Contents, Medline). Database searching of nucleic acids and proteins (BLAST, Fasta). Sequence alignments (Blast, ClustalW). Gene finding (GeneMark, Glimmer). Functional genomics. Genome research (human genome, Drosophila, mouse, Saccharomyces, Arabidopsis). Specialized software for molecular biology. Sequence analysis (DNASIS). Analysis of electropherograms (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further Comments

The course is taught annually.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

The course is taught annually.
The course is taught: every other week.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Bioinformatics I - nucleic acids

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Prerequisites

( Bi4010 Essential molecular biology || Bi4020 Molecular biology ) && NOW( Bi9060 Bioinformatics II )
Basic course of molecular biology (eg. Bi4020).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Analytical Biochemistry (programme PřF, N-BCH)
• Mathematical Biology (programme PřF, B-BI)
• Mathematical Biology (programme PřF, N-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• General Biology (programme PřF, N-BI)

Course objectives

The aim of this course is to understanding principles of the computational tools for analysis of nucleic acids and protein sequences. Students should be able to exploit information resources for molecular biology available on internet, i.e. molecular biology databases and different computational tools for their analysis. At the end of the course the students are able manipulate in silico with nucteotide and protein sequences, design primers, perform pair and multiple sequence comparisons and phylogenetical studies, anotate newly determined sequences and submit sequences to public databases.

Syllabus

• Databases for molecular biology.
• DNA sequencing techniques.
• Manipulation with sequence data.
• Tools for local sequence alignment.
• Multiple alignment.
• Comparative genomics.
• Computational gene finding.
• Protein identification databases.
• Prediction of secondary RNA structure.
• Submiting of genomic sequence to primary database.
• Phylogenetic analysis based on nucleotide and protein sequences.
• Image analysis of 1D electrophoretic gels.

Literature

• CVRČKOVÁ, Fatima. Úvod do praktické bioinformatiky. Praha: Academia, 2006, 150 pp. ISBN 80-200-1360-1. info
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Teaching methods

Weekly lectures and exercises, homeworks concerning each practical topic.

Assessment methods

Examination is based on written test composed of 20 questions. Correct answering of at least 60% of them is required to pass the test and a practical exam on PC where the applicant solve 2 practical bioinformatics tasks.

Language of instruction

Czech

Follow-Up Courses

• Bi9060 Bioinformatics II – proteins
• Bi9061 Bioinformatics - practice

Further Comments

The course is taught annually.
The course is taught: every other week.

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

Bi5000 Introduction to bioinformatics

Extent and Intensity

1/1/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Roman Pantůček, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Roman Pantůček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Roman Pantůček, Ph.D.

Prerequisites

Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology
Basic course of molecular biology (eg. Bi4020, B4030, B3120 or B7940).

Course Enrolment Limitations

The course is only offered to the students of the study fields the course is directly associated with.

fields of study / plans the course is directly associated with

• Cellular and Molecular Diagnostics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, B-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)

Course objectives

Cílem kurzu je zvládnutí běžných aplikací potřebných pro zpracování diplomové práce z molekulární biologie, především seznámení posluchačů s informačními službami pro molekulární biologii (molekulárně biologické databáze a nástroje pro jejich využití).

Syllabus

• Informační služby v počítačových sítích - využití v molekulární biologii a genetice. Prohledávání citačních databází (PubMed, WOS). Sekvencování DNA, metody analýzy genomů. Manipulace se sekvenčními daty (převody formátů sekvencí, restrikční analýza, návrh primerů). Stanovení podobnosti sekvencí (dot-plot, BLAST, Fasta). Mnohonásobné porovnávání sekvencí (ClustalW). Hledání genů a funkčních oblastí (GeneMark, Glimmer). Analýza sekvencí proteinů, databáze konzervativních domén proteinů. Funkční genomika. Predikce sekundární struktury RNA. Specializované programy pro molekulární biologii. Analýza elektroforetických gelů (GelCompar).

Literature

• Viz webová stránka předmětu.
• Bioinformatics : methods and protocols. Edited by Stephen Misener - Stephen A. Krawetz. Totowa, New Jersey: Humana Press, 2000, xi, 500 s. ISBN 0-86903-732-0. info
• ATTWOOD, Teresa K. and David J. PARRY-SMITH. Introduction to bioinformatics. 1st pub. Essex: Longman, 1999, xx, 218. ISBN 0582327881. info
• Bioinformatics : a practical guide to the analysis of genes and proteins. Edited by Andreas D. Baxevanis - Francis B.F. Ouellette. New York: Wiley-Interscience, 1998, xiv, 370 s. ISBN 0-471-19196-5. info

Assessment methods (in Czech)

Výuka probíhá každý týden v počítačové učebně COMPB. Pro ukončení je požadováno zpracování samostatné zápočtové práce dle zadaného tématu.

Language of instruction

Czech

Follow-Up Courses

• B7201 Praktikum základů genomiky
• B8020 Biophysical properties and computer analysis of nucleic acids, proteins, genes and genomes

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: omezení se vztahuje na 1 hod. cvičení v učebně COMPB, nikoli na přednášku

Listed among pre-requisites of other courses

• Bi5000c Bioinformatics - practice
  Bi5000 || NOW(Bi5000) && !Bi9061  

Teacher's information

http://orion.sci.muni.cz/kgmb/bioinformat/

• Enrolment Statistics (recent)