|Thursday||10:30 AM - 12:30 PM||lesson||Lecture Hall L|
|Friday||1:30 PM - 4:30 PM||lesson||Lecture Hall H|
|Friday||4:30 PM - 5:30 PM||lesson||Lecture Hall H||from Oct 30, 2015 to Jan 29, 2016|
1. to learn about some basic problems and algorithms behind common bioinformatics applications (sequence alignment, sequence similarity, phylogenetics), and 2. to get an idea of some basic computational issues (problem specification, efficiency of algorithms, limitations).
Introduction to algorithm analysis: running time and storage space analysis; notation for complexity analysis: Big-Oh-notation, growth of functions; formalism on strings/sequences; basic combinatorics on strings;
Applications; Pairwise sequence alignment: Exhaustive search, Dynamic programming (DP) algorithm of Needleman-Wunsch (global alignment), DP algorithm of Smith-Waterman (local alignment), other variants; multiple sequence alignment: DP algorithm and heuristics; Scoring matrices: PAM (computation, application); Heuristics for sequence alignment and database search: BLAST; string distance and similarity, edit distance;
Introduction to graphs and trees; number of phylogenetic trees; distance-based data: algorithm UPGMA; character-based data: Perfect Phylogeny (PP), Small parsimony: Fitch' algorithm; Large parsimony: heuristics.
Written exam, followed by oral exam.
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