----------------------------------------------------------------------------- Syllabus of a bioInformatic course for computer science students Ron Appel and Amos Bairoch 1997-1998 ----------------------------------------------------------------------------- Aim: general introduction in computer analysis of biological macromolecules Who is giving it: R. Appel HUG ron.appel@dim.hcuge.ch A. Bairoch Fac. Medecine bairoch@cmu.unige.ch G. Bittar HUG bittar@sc2.unige.ch P. Bucher ISREC Lausanne pbucher@isrec-sun1.unil.ch B. Chopard CUI chopard@cui.unige.ch M. De Francesco Glaxo mdf12736@ggr.co.uk E. Gasteiger Fac. Medecine gasteige@cmu.unige.ch N. Guex Glaxo ng45767@ggr.co.uk R. Milanese CUI milanese@cui.unige.ch M. Peitsch Glaxo mcp13936@ggr.co.uk C. Pellegrini CUI pell@cui.unige.ch When: Each week, Wednesday, 10:15 to 12:30 AM - General biological introduction Given by: A. Bairoch, N. Guex o Definition and components of living systems o DNA -> genes -> chromosomes (exons/introns; coding/non-coding) -> genomes (size, complexity) o Amino acids -> proteins -> proteomes o Tertiary structure of biomolecules o Molecular evolution o The tree of life: prokaryotes, eukaryotes, archaebacteria, viruses Time: 3 h 29 October + 5 November - Why and how do molecular biologists use computational resources Given by: A. Bairoch [BEND9601] Time: 1 h 5 November - Databases Given by: R. Appel and A. Bairoch o Inventory of the databases used by molecular biologists. What are the various types (DNA and Protein sequences db., Genomic, 3D, 2D-PAGE, etc.) [DAMT9201] [See http://expasy.hcuge.ch/amos_www_links.html] o Format (flat file structured or not, relational, Object Oriented) o Distributions (tape, CD, Internet, the WWW paradigm) [HARP9401, HARP9501, HARP9601] o Updating problems o Integration of data resources (cross-referencing, federating, CORBA) [APPR9602] Time: 8 h 12 November, 19 Novembre, 26 November, 3 Decembre - Algorithms for primary sequence analysis Given by: R. Appel and A. Bairoch o Based on string/word searches (patterns, PROSITE, restriction sites) [BORK9602, BARG9001, JIAK9101] o Based on sliding windows (hydrophobicity, transmembrane regions, coiled-coil domains, etc.) [CLAJ9101, KYTJ8201, EISD8402, RAOJ8601, LUPA9101] o Based on weight matrices (profiles) [BORK9601, BUCP9401] o Based on classical statistic methods such as determinant analysis and other multivariate techniques (codon usage, functional classification by amino acid composition, etc.) [KLEP8602, GOUM8201, SHAP8701] o Based on graphical representations (sequences 'logo', chaos game representations, vector representation of sequences, etc.) [SCHT9001, DUTC9201, GOLN9301, HAME8901, PICC8701] Time: 6 h 10 December, 17 December, 14 January - Similarity searches Given by: B. Chopard and R. Milanese with help from P. Bucher o Definition of the problem, historical perspective (Needleman and Wunsch, Waterman and Smith, Pearson, Brutlag, Altschul, etc.) [ALTS9401] o Optimal two way alignments using dynamic programming o Amino acid substitution matrices [ALTS9101, GONG9401, HENS9201, HENS9302, JONE9201, TAYW9301, VOGG9501] o Gap penalization [LESA8603, ALTS8903, THOD9501] o Optimization of the method: FASTA, Blast [PEAW8801, PEAW9101, PEAW9102, PEAW9501, ALTS9001, ALTS9002, ALTS9401] o Parrallelization of WS: multiple processor approaches and specialized hardware [COUA8701, BRUD9301, HUAX9201, JUEA9501, MILP9101] o Dot matrices [BOGM9203, GRAN9001, SHEV9101, SHEV9401] Time: 8 h 21 January, 28 January, 4 February, 11 February - Multiple alignements Given by: B. Chopard and R. Milanese with help from P. Bucher o Definitions of the problems and historical perspective [CHAS9201] o Clustering methods (UPGMA, etc.) o Rigorous dynamic programming, simulated annealing [HIGD8801, THOD9402] Time: 6 h 11 March, 18 March, 25 March - Phylogenetic analysis Given by: G. Bittar o Definition and history of phylogenetic analysis o Distance computations o Parsimony methods o Maximum likelihood methods o Bootstraping Time: 4 h 1 April, 8 April - Computational problems in structural analysis Given by: Glaxo (M. Peitsch and/or N. Guex) o Definition of structural elements in proteins (helix, turn, beta-sheet) and in DNA/RNA (hairpin, loop, B/Z helix, etc.) o Introduction to energy constraints in tertiary structures o Protein secondary structure prediction [BARG9501] o RNA secondary structure prediction o 3D modelling by homology [PEIM9502] o De novo 3D prediction [BENS9301] o 3D prediction by threading Time: 8 h 22 April, 29 April, 6 May, 13 May - Computational approaches to help in experimental approaches Given by: R. Appel o Protein separation and characterization by 2-D PAGE (introduction; basic computer problems such as scanning, image processing, spot detection, quantitation; advanced problems such as clustering) o Protein characterizations (Mass Spectrometry software, identification of proteins by composition, by proteolytic digests) Time: 4 h 20 May, 27 May - Advanced computational techniques in molecular biology Given by: C. Pellegrini with M. De Francesco o Use of neural networks (exon/intron detection, secondary structure prediction, post-translational modifications) [RECM9402] o Knowledge based systems (enzymatic pathways, genome evolution) [BRUD9101] o Advanced statistical approaches: Hidden Markov Models (HMM) (domains detection, gene identification) [BALP9401, BORM9402, BORM9501, CHUG9201, EDDS9501, HUBT9501, KROA9401, MITG9501] o Genetic algorithms (contig assembly, structure prediction) [DANT9401, HERF9401, PARR9301] Time: 6 h 3 June, 10 June, 17 June Total: 54 h General textbooks ================= Doolittle R.F. Of URFs and ORFs: a primer on how to analyze derived amino acid sequences. University Science Books, Mill Valley California, (1986). von Heijne G. Sequence analysis in molecular biology. Treasure trove or trivial pursuit. Academic Press, London, (1987). Sequence analysis primer. Gribskov M., and Devereux J., Editors, MacMillan, London, (1991). Computational methods in genome research. Suhai S., Editor, Plenum Press, New York, (1994). Biocomputing. Informatics and genome projects. Smith D.W., Editor, Academic Press, New-York, (1994).