Projects 786102

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Projects 786-102

• Spring 2002

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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

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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)

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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

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I Retrieval parsing

• Bioperl. www.bio.perl.org
• Biopython. www.biopython.org

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II Gene recognition

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

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III Gene annotation

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

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IV Pattern recognition

• Teiresias algorithm and the Bio-Dictionarywww.res
  earch.ibm.com/bioinformatics/

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V Sequence alignment

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

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VI Protein structure prediction

• PredictProtein
• BMERC
• PredictProtein
• GenThreader, mGenThreader

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VII CASP

• CASP Protein structure prediction competition.
  http//predictioncenter.llnl.gov/

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VIII Gene expression

• SAGE. http//www.ncbi.nlm.nih.gov/SAGE/
• GeneCluster
• Others can be found athttp//genome-www5.stanfor
  d.edu/MicroArray/SMD/restech.html

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Phylogenetic trees

• Phylip
• Nexus
• Tree-Puzzle