Bi5000 Bioinformatics

Faculty of Science
Autumn 2024
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
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
Teacher's information
https://loschmidt.chemi.muni.cz/bioinf/
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.
  • Enrolment Statistics (recent)
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