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Projects – 786-102

Projects – 786-102. Spring 2002. Procedure. Groups of four (in general) Three meetings with instructor (or more as desired) For each meeting: 1-2 page progress report After each meeting, 5 minute class report End of term: 45 minute oral presentation, and written report. Rough schedule.

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Projects – 786-102

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  1. Projects – 786-102 Spring 2002

  2. Procedure • Groups of four (in general) • Three meetings with instructor(or more as desired) • For each meeting: 1-2 page progress report • After each meeting, 5 minute class report • End of term: 45 minute oral presentation,and written report

  3. Rough schedule • Brief description of topic. Initial literature / source search. Division of labor within the team. (March 13-15) • Some substantive results. Outline of final project. (April 3-5) • Draft of final (with holes still to be filled).(April 17-19) • Final: written and class presentation. (April 26, May 3)

  4. Project content These are guidelines only. Adapt as needed. • Statement of problem, motivation. 10% • Literature and/or code. 15% • Algorithm(s). 35% • Examples. 20% • Evaluation. 10% • Open problems. 10%

  5. I Retrieval & parsing • Bioperl. www.bio.perl.org • Biopython. www.biopython.org

  6. II Gene recognition • Procrustes. www-hto.usc.edu/software/procrustes/ • HMMgene • Genscan • FGENEH • NetGene2 • Grail • GeneMark • GeneMark HMM • Genie • GenLang • GeneID

  7. III Gene annotation • BioCoREhttp://www.ebi.ac.uk/research/cgg/services/ • Distributed Sequence Annotation System (DAS) http://stein.cshl.org/das/

  8. IV Pattern recognition • Teiresias algorithm and the Bio-Dictionarywww.research.ibm.com/bioinformatics/

  9. V Sequence alignment • Multiple sequence alignment. Clustalw • Blast • Fasta • Smith-Waterman.www-hto.usc.edu/software/seqaln/seqaln-query.html

  10. VI Protein structure prediction • PredictProtein • BMERC • PredictProtein • GenThreader, mGenThreader

  11. VII CASP • CASP – Protein structure prediction competition. http://predictioncenter.llnl.gov/

  12. VIII Gene expression • SAGE. http://www.ncbi.nlm.nih.gov/SAGE/ • GeneCluster • Others can be found at:http://genome-www5.stanford.edu/MicroArray/SMD/restech.html

  13. Phylogenetic trees • Phylip • Nexus • Tree-Puzzle

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