Course Information

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.

Timetable

Fri 12:00–13:50 C525

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 46 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

Study Materials

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.

Timetable

Fri 8:00–9:50 C525

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 44 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

Study Materials

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.

Timetable

Wed 18:00–19:50 B410

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 44 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

Study Materials

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.

Timetable

Fri 12:00–15:50 B117

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themself familiar with the linux operating system.

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 39 fields of study the course is directly associated with, display

Course objectives

The assumption that all species, extant and extinct, evolved from a single common ancstor species forms the basis of phylogenetic research. By comparing both DNA and protein sequences, it is one key aspect of applied bioinformatics to reconstruct when and in which order the corresponding species have emerged. In this course we will detail on our current understanding of how biological sequences change over time. We will present methods to infer a phylogenetic tree from DNA and protein sequences and how to test the significance of this reconstruction. Particular attention will be given to how to compile an informative data set from the millions of different sequences available in the public databases. Eventually, we will discuss to what extent the evolution of biological sequences is informative for the evolution of species. The course will cover both a theory part and practical exercises where the students will have hands-on training on phylogeny reconstruction in a computer lab.

Syllabus

• The course will deal with the following topics: 1) The molecular basis of evolution. A primer of molecular genetics. 2) Introduction into basic population genetics and the coalescent model. 3) Modelling sequence evolution. 4) Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference. 5) Biological Sequence databases

Literature

• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info
• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info

Assessment methods

exercices and written exam

Language of instruction

English

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Engersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.

Timetable

Fri 30. 11. 15:00–16:50 A107, 16:00–19:50 B130, Sat 1. 12. 10:00–11:50 A107, 11:00–13:50 B130, Tue 4. 12. 14:00–17:50 B204, Wed 5. 12. 15:00–18:50 B311, Fri 7. 12. 17:00–18:50 A107, 17:00–20:50 B130, Sat 8. 12. 10:00–11:50 A107, 11:00–13:50 B130

Prerequisites (in Czech)

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themself familiar with the linux operating system.

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 41 fields of study the course is directly associated with, display

Course objectives (in Czech)

The assumption that all species, extant and extinct, evolved from a single common ancstor species forms the basis of phylogenetic research. By comparing both DNA and protein sequences, it is one key aspect of applied bioinformatics to reconstruct when and in which order the corresponding species have emerged. In this course we will detail on our current understanding of how biological sequences change over time. We will present methods to infer a phylogenetic tree from DNA and protein sequences and how to test the significance of this reconstruction. Particular attention will be given to how to compile an informative data set from the millions of different sequences available in the public databases. Eventually, we will discuss to what extent the evolution of biological sequences is informative for the evolution of species. The course will cover both a theory part and practical exercises where the students will have hands-on training on phylogeny reconstruction in a computer lab.

Syllabus (in Czech)

• The course will deal with the following topics: 1) The molecular basis of evolution. A primer of molecular genetics. 2) Introduction into basic population genetics and the coalescent model. 3) Modelling sequence evolution. 4) Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference. 5) Biological Sequence databases

Language of instruction

English

Further Comments

Study Materials
The course is taught only once.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2018

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

doc. RNDr. Aleš Horák, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 37 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2017

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

doc. RNDr. Aleš Horák, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 37 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2016

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

doc. RNDr. Aleš Horák, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 37 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2015

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

doc. RNDr. Aleš Horák, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 37 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2014

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 36 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2013

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 36 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

IV116 Applied bioinformatics: The Evolutionary relationships of genes and species

The course is not taught in Autumn 2012

Extent and Intensity

1/1/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

Dr. Ingo Ebersberger (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)
Dr. Greg Ewing (lecturer), doc. Ing. Matej Lexa, Ph.D. (deputy)

Guaranteed by

prof. Ing. Václav Přenosil, CSc.
Department of Machine Learning and Data Processing – Faculty of Informatics
Contact Person: doc. Ing. Matej Lexa, Ph.D.
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics

Prerequisites

Basic knowledge of molecular biology or bioinformatics will be helpful. Students should make themselves familiar with the Linux operating system.

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 36 fields of study the course is directly associated with, display

Course objectives

In this course we will detail on our current understanding of how biological sequences change over time.
At the end of the course, the student will:
be able to use methods to infer a phylogenetic tree from DNA and protein sequences
know how to test the significance of phyllogenetic tree reconstruction
be able to extract useful datasets from sequences available in the public databases
understand the difference between evolution of biological sequences and the evolution of species

Syllabus

• The course will deal with the following topics:
• The molecular basis of evolution. A primer of molecular genetics.
• Introduction into basic population genetics and the coalescent model.
• Modelling sequence evolution.
• Methods for phylogenetic tree reconstruction. Maximum Parsimony, Maximum Likelihood, Bayesian Inference.
• Biological Sequence databases

Literature

• PAGE, Roderic D. M. and Edward C. HOLMES. Molecular evolution :a phylogenetic approach. Oxford: Blackwell Science, 1998, v, 346 s. ISBN 0-86542-889-1. info
• ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info

Teaching methods

lectures and computer exercises

Assessment methods

exercises and written exam

Language of instruction

English

Further comments (probably available only in Czech)

The course is taught: in blocks.

Teacher's information

http://www.cibiv.at/

• Enrolment Statistics (recent)