Introduction to computational biology 1000-2N03BO
1. Short introduction to molecular biology (nucleic acids, proteins, transcription, translation, experimental techniques). (2 lectures).
2. Sequence alignment (global -- Needelman Wunsh algorithm and local -- Smith-Watermann algorithm). (2 lectures).
3. Amino acid substitution matrices (PAM, BLOSUM), efficient sequence comparison methods (BLAST, FASTA), Statistical significance of alignment scores. (3 lectures).
4. Hidden Markov Models (Viterbi and Baum-Welch method) with applications. (2 lectures).
5. Multiple alignment (dynamic programming, `star alignment', `tree alignment'), profile analysis, approximation algorithms, progressive alignment (CLUSTALW), Tcoffee, MAFFT( 2 lectures).
6. Genome-scale alignment. (1 lecture).
7. Introduction to phylogenetics. (2 lectures).
The course will be given in Polish, if no non-polish speaking students register for it.
Type of course
Course coordinators
Term 2023L: | Term 2024L: |
Learning outcomes
knowledge:
1. Student has a general knowledge of the problems of computational biology.
2. Student has a basic knowledge of the mathematical tools used in the modeling and analysis of molecular data.
skills:
1. Student can perform a simple bioinformatic analysis for molecular sequences.
2. Student can use advanced bioinformatics tools.
competence:
1. knows his own limitations of knowledge and understands the need for further education (K_K01)
2. is able to manage their time and make commitments and meet deadlines (K_K05)
3. can use the interdisciplinary literature
Assessment criteria
Programming assignments,
written test,
Oral exam.
Bibliography
1. A. Malcolm Campbell. Laurie J. Heyer, Discovering Genomics, Proteomics, and Bioinformatics, Pearson Education 2003,
2. R. Durbin, S. Eddy, A. Krogh, G. Mitchson, Biological Sequence Analysis, Cambridge Univ. Press, 1997.
3. P. Pevzner, Computational Molecular Biology, The MIT Press, 2000
4. Ewens, W.J. and Grant, G., Statistical Methods in Bioinformatics, Springer-Verlag, 2001
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:
- Bachelor's degree, first cycle programme, Computer Science
- 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: