S1006 Bioinformatics - Sequence and Structure Analysis

Faculty of Science
Spring 2015
Extent and Intensity
2/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
dr Hedvig Hegyi, PhD. (lecturer)
Guaranteed by
prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
- A proper understanding of English - A sufficient knowledge of a Unix-like operating system
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
- Understand and learn the basic concepts in bioinformatics
- Understand DNA and protein sequences, genomes and proteomes
- Be able to carry out database searches using the BLAST programs
- Be able to do sequence analysis on their own, using the Clustalw/Muscle programs
- Find the domain composition of a protein sequence
- Determine the intrinsic disorder of a protein
Syllabus
  • Sequence databases, DNA and protein sequences, database searches
  • - historical overview, the first databases of protein and DNA sequences
  • - sequence retrieval using NCBI's Entrez
  • - fully sequenced genomes in the three kingdoms of life
  • - genomes and genome browsers
  • - fast database searches: FastA & the BLAST programs
  • Sequence analysis, pairwise and multiple sequence alignments
  • - pairwise alignments, global and local
  • - basic algorithms: Needleman-Wunch, Smith-Waterman
  • - the purpose of sequence alignments: structural, functional, evolutionary information
  • - multiple alignment programs, clustalw & muscle
  • - evolutionary trees
  • - orthologs and paralogs
  • Protein structure, structural databases, protein structure prediction
  • - The Protein Data Bank
  • - Protein structure prediction from sequence, the CASP experiments
  • - Secondary Structure analysis
  • Protein domains, protein classification systems, protein stability, alternative splicing
  • - globular domains
  • - structural classification of proteins, SCOP & CATH
  • - Alternative splicing and protein structure stability
  • Intrinsic protein disorder, prediction and functional aspects
  • - Discovery of protein disorder
  • - Predicting disorder from sequence
  • - Protein disorder in alternative splicing & cancer
  • - Organism complexity and protein disorder
  • - Functional advantages of disorder
Literature
    recommended literature
  • MOUNT, David W. Bioinformatics : sequence and genome analysis. 2nd ed. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004, xii, 692. ISBN 0879697121. info
Teaching methods
lectures
Language of instruction
English
Further comments (probably available only in Czech)
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms spring 2012 - acreditation, Spring 2016.
  • Enrolment Statistics (Spring 2015, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2015/S1006