Scribe: L. Heath

Today's Handouts and Announcements

• No handouts.

Today's Topics

• Douglas Slotta began a discussion of the maximum likelihood approach for constructing phylogenetic trees, which was completed in class the next day.

• Subhag Oak began a discussion of Issues in Searching Molecular Sequence Databases and tools for comparing and aligning molecular sequences. He covered these topics:

  • Algorithms: Smith-Waterman

  • Scoring systems: PAM and BLOSUM

  • Alignment statistics

  • The issue of database redundancy

  • Tools:
    • AUTOMAT --- Based on BLAST ideas. Where BLAST extends seeds, AUTOMAT links them.
    • SALSA (Searching with Assembly of Local Sequence Alignment)

Today's Sources

• Setubal and Meidanis: Chapters 3 and 6.

• Salzberg, Searls, and Kasif: None.

• Joseph Felsenstein
  Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach
  Journal of Molecular Evolution 17, 1981, 368-376.

• S.F. Altschul, M.S. Boguski, W. Gish, and J.C. Wootton
  Issues in searching molecular sequence databases
  Nature Genetics 6, February 1994, 119-129.

• H. Cantalloube, et al.
  Automat and BLAST: comparison of two protein sequence similarity search programs
  Comput Appl Biosci. 11, June 1995, 261-272.

• T. Rognes and E. Seeberg
  SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments.
  Bioinformatics 14, 1998, 839-845.