Algorithms in bioinformatics

Course Description

Basic facts on biological sequences. Sequential string search. Boyer-More algorithm. Indexed string search. Suffix tree. Suffix array. Approximate string search. String distances. Dynamic programming. Global and local alignment. Gaps, weights, substitution matrices. Multiple alignment, profiles, families. Algorithms in programs for sequence database searches FASTA, BLAST, GBLAST, BLAT. Problems in genome sequencing. Fragment assembly. Motif discovery. Tandem repeats. Phylogenetic trees.

Study Programmes

Post-graduation study

Literature

(.), Dan Gusfield: Algorithms on Strings, Trees and Sequences, Cambridge University Press, 1997.,
(.), Arthur M. Lesk: Introduction to Bioinformatics, Oxford University Press, 2002.,
(.), Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 2003.,

General

ID 154682
  Winter semester
6 ECTS