Syllabus for CMP/BIO 243 Bioinformatics

Topics for week beginning on specified date. (Note: This schedule is too ambitious. These dates will surely slip by at least a week as the quarter unfolds.)

1. (Sept 27): Introduction to molecular biology and biosequence databases.
2. (Oct 4): String searching and probability/statistical significance. Application: BLAST and FASTA searches with CASP2 targets and pieces of recently sequenced DNA
3. (Oct 11): pairwise alignment, profiles, Bayesian statistical methods. Application: repeat above searches with Smith-Waterman, find promoters, splice sites and protein motifs with BLOCKS profiles
4. (Oct 18): multiple alignment, simple Markov models, statistical models and parameter estimation. Application: CLUSTALW multiple alignment of globins and some more difficult to align protein family of current interest, GENMARK genefinder
5. (Oct 25): hidden Markov models, expectation maximization. Application: HMMs for protein families, finding remote homologs of CASP2 targets using our HMM library, multiple alignment with HMMs
6. (Nov 1): neural nets, generalized HMMs for genefinding. Application: comparison of GENIE and GRAIL on human DNA
7. (Nov 8): grammars and RNA secondary structure. Application: determine/model secondary structure for tRNA and snRNAs
8. (Nov 15): protein structure, homology modeling, threading, energy minimization. Application: Try one of the existing threading web sites with CASP2 sequences, compare to UCSC HMM predictions
9. (Nov 22): phylogeny. Application: Use PHYLIP programs to compare DNA of humans, gorilla and chimps
10. (Dec 2): future directions.

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