- Inter-faculty Studies in Bioinformatics and Systems Biology
- Bachelor's degree, first cycle programme, Computer Science
- Bachelor's degree, first cycle programme, Mathematics
- Master's degree, second cycle programme, Bioinformatics and Systems Biology
- Master's degree, second cycle programme, Computer Science
- Master's degree, second cycle programme, Mathematics
Bioinformatics 1200-BIOINF-OG
The aim of this course is to provide a wide overview of bioinformatics methods working on sequence and structural data.
Lots of attention will be put to understanding the basis of bioinformatics. The most popular web-services, software and databases will be presented
1) Introduction
What is bioinformatics. Its role and importance in biology, medicine, pharmacology, biotechnology and drug design.
2) Bioinformatical databases
GenBank, SwissProt, PDB, PFAM and other databases, hosting sequences, structures and annotations. The issues of data quality, redundancy and completness. The most popular file formats (PDB, FASTA)
3) Structure visualization Pymol, VMD and other popular software
4) Optimal sequence alignment
Computational complexity of the problem. Differences between local and global alignment. Gap penalty model, substitution matrices. The problem of alignment significance estimation: alignment score, e-value, p-value, z-score, sequence identity
5) Homology and protein families
The concepts of a homolog, paralog, ortholog and analog.
6) Heuristical sequence alignment methods and adta base search: FASTA and BLAST
7) Multiple sequence alignments (MSA)
Computational complexity of the problem, example heuristical methods: CLUSTAL, mafft, muscle. Phylogenetic trees. Bazy danych PROSITE and PFam databases.
8) Sequence profiles: significance and applications
Hidden Markov Models (HMM). PsiBlast, HMMER, HHSearch programs. Alignment of sequence profiles (1D threading)
9) Analysis and comparison of protein structures
Optimal structure superimposition. Mean root square coordinate difference (crmsd). methods for definition (DSSP) and prediction of secondary structure (PsiPred)
10) Predicting protein structure and function
Different concepts for protein threading. Servers and metaservers. Comparative modeling and de novo approach.
Popular software: Rosetta, SWISS-MODEL i MODELLER. Ligand docking and structure based drug design
Main fields of studies for MISMaP
biotechnology
physics
computer science
biology
Type of course
Mode
Prerequisites (description)
Course coordinators
Learning outcomes
Student posses general knowledge of the basic problems and techniques of bioinformatics (sequence and structure databases, sequence and structure comparisons, computational methods of bioinformatics). Practical knowledge of applications of bioinformatics in molecular modeling of proteins and nucleic acids, in particular a student can:
- find a given structure in the PDB and collect necessary informations about it
- calculate an alignment between two sequences
- find homologues sequences in databases; restrict the search by various criteria
- assign a protein to a protein family; both according to its structure and sequence
- find plausible templates for comparative modeling
- build a structural model of a query protein by means of comparative modeling
Assessment criteria
Written test, containing 15 closed questions and 5 open questions, conducted off-line (in a class room) or an oral exam - possibly online
Practical placement
does not concern
Bibliography
1. A. D. Baxevanis, B.F. F. Ouellettee, Bioinformatics, Wiley 1998
2.J. Setubal, J. Meidanis, Introduction to Computational Biology, PWS Publishing, 1997
3.E. V. Koonin, M. Y. Galperin, Sequence-Evolution-Function, Computational Approaches in Compartive Genomics, Kluwer, 2003
Additional information
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:
- Inter-faculty Studies in Bioinformatics and Systems Biology
- Bachelor's degree, first cycle programme, Computer Science
- Bachelor's degree, first cycle programme, Mathematics
- Master's degree, second cycle programme, Bioinformatics and Systems Biology
- Master's degree, second cycle programme, Computer Science
- Master's degree, second cycle programme, Mathematics
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: