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

Postgraduate doctoral study programme

Literature

Dan Gusfield (1997.), Algorithms on Strings, Trees and Sequences, Cambridge University Press
Arthur Lesk (2014.), Introduction to Bioinformatics, Oxford University Press
Richard Durbin, Sean R. Eddy, Sean Eddy, Anders Krogh, Graeme Mitchison (1998.), Biological Sequence Analysis, Cambridge University Press

For students

General

ID 154682
  Winter semester
6 ECTS
L0 English Level