# Algorithms and programming languages for bioinformatics (2011/2012)

### Course partially running (all years except the first)

Course code
4S000525
Credits
12
Coordinator
Zsuzsanna Liptak
Teaching is organised as follows:
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

### Learning outcomes

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).

### Syllabus

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).

### Assessment methods and criteria

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).

#### Statistics about transparency requirements (Attuazione Art. 2 del D.M. 31/10/2007, n. 544)

 Outcomes Exams Outcomes Percentages Average Standard Deviation Positive 72.72% 27 2 Rejected 9.09% Absent -- Ritirati 15.15% Canceled 3.03%
 18 19 20 21 22 23 24 25 26 27 28 29 30 30 e Lode 0.0% 0.0% 0.0% 4.1% 4.1% 4.1% 0.0% 4.1% 16.6% 16.6% 20.8% 16.6% 12.5% 0.0%

Data from AA 2011/2012 based on 33 students. I valori in percentuale sono arrotondati al numero intero più vicino.