Algorithms and programming languages for bioinformatics - ALGORITMI PER BIOINFORMATICA (2013/2014)

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Course code
4S000525
Name of lecturer
Zsuzsanna Liptak
Number of ECTS credits allocated
6
Academic sector
INF/01 - INFORMATICS
Language of instruction
English
Location
VERONA
Period
II semestre dal Mar 3, 2014 al Jun 13, 2014.
Web page
http://profs.sci.univr.it/~liptak/ALBioinfo/
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To show the organization of the course that includes this module, follow this link * Course organization

Lesson timetable

Learning outcomes

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).

Syllabus

ALGORITHM ANALYSIS

Introduction to algorithm analysis: time and storage space analysis; notation for complexity analysis: Big-Oh-notation, growth of functions; formalism on strings/sequences; basic combinatorics on strings;

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); multiple sequence alignment; Scoring matrices: PAM (computation, application); Heuristics for sequence alignment: dotplots, q-grams, FASTA, BLAST;

PHYLOGENETICS

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 (descriptive statistics; hypothesis testing, P-values, type I and II errors).

Assessment methods and criteria

Written exam and presentation of a project.

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