Unit | Credits | Academic sector | Period | Academic staff |
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LINGUAGGI PER BIOINFORMATICA | 6 | INF/01-INFORMATICS | See the unit page | See the unit page |
ALGORITMI PER BIOINFORMATICA | 6 | INF/01-INFORMATICS | II semestre |
Zsuzsanna Liptak
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Module: LINGUAGGI PER BIOINFORMATICA
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Module: ALGORITMI PER BIOINFORMATICA
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1. to learn about some basic problems and algorithms behind common bioinformatics applications (alignment, sequence similarity, phylogenetics), and 2. to get an idea of some basic computational issues (complexity, efficiency, limitations).
Module: LINGUAGGI PER BIOINFORMATICA
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Module: ALGORITMI PER BIOINFORMATICA
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SEQUENCE ALIGNMENT
Applications; Pairwise sequence alignment: Exhaustive search, Dynamic programming (DP) algorithm of Needleman-Wunsch (global alignment), DP algorithm of Smith-Waterman (local alignment), other variants (sketch); Formalism on strings/sequences; Scoring matrices: PAM (computation, application); Heuristics for sequence alignment: dotplots, q-grams, FASTA, BLAST;
STRING SIMILARITY AND DISTANCE
String similarity and distance: percent similarity, edit distance, Hamming distance, connection between edit distance and alignment score;
ALGORITHM ANALYSIS
Introduction to algorithm analysis: time and storage space analysis; notation for complexity analysis: Big-Oh-notation, growth of functions;
PHYLOGENETICS
History of systematics; Introduction to graphs and trees; number of phylogenetic trees; distance-based data: UPGMA; character-based data: Perfect Phylogeny (PP), Small parsimony: Fitch' algorithm; Large parsimony: heuristics (sketch);
STATISTICS
Some basic statistics (hypothesis testing, P-values, type I and II errors, descriptive statistics).
Module: LINGUAGGI PER BIOINFORMATICA
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Module: ALGORITMI PER BIOINFORMATICA
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Written exam: 50%, and presentation of a project (talk with digital slides): 50%
The written exam can be taken in two parts (midterm and final), in which case both have to be passed; or in one (complete final exam).
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