Scribe: L. Heath

Today's Handouts and Announcements

• Last day of class. All coursework needs to be submitted by Friday morning.

Today's Topics

• Chad Wingrave discussed Motifs --- conserved sequences in protein families. Some of the topics he covered:

  • Representations for motifs
    • Regular expressions
    • Hidden Markov Models (HMMs)
    • Blocks (one conserved sequence)
    • Prints (several conserved sequences)

  • Databases of protein information
    • GenBank
      The database of "everything" at NCBI.
    • SWISS-PROT
      A non-redundant, curated database of protein families.
    • TrEMBL
      A computer-annotated supplement to SWISS-PROT.
    • OWL
      A nonredundant composite of 4 public databases.
    • Protein Information Resource (PIR)
    • NRL-3D
      A protein sequence and structure database.

  • Databases of protein motifs
    • PROSITE
      Uses experts to build protein families from SWISS-PROT.
    • Pfam
      Uses Hidden Markov Models to represent protein families.
    • ProDOM
      Fully automatic construction of protein families.
    • PRINTS
      Expert moderated compendium of protein fingerprints.
    • Blocks+
      Blocks are generated by PROTOMAT, using scoring with a PAM matrix.
    • InterPro
      A combination of a number of sources of protein data.

Today's Sources

• Setubal and Meidanis: None.

• Salzberg, Searls, and Kasif: None.

• Steven Henikoft, Jorja G. Henikoft, and Shmuel Pietrovski
  Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
  Bioinformatics 15, 1999, 471-479.

• F. Corpet, J. Gouzy, and D. Kahn
  Recent improvements of the ProDom database of protein domain families
  Nucleic Acids Research 27, January 1 1999, 263-267.
  Also available locally as a PDF file.

• T.K. Attwood, D.R. Flower, A.P. Lewis, J.E. Mabey, S.R. Morgan, P. Scordis, J.N. Selley, and W. Wright
  PRINTS prepares for the new millennium
  Nucleic Acids Research 27, January 1 1999, 220-225.
  Also available locally as a PDF file.

• A. Bateman, E. Birney, R. Durbin, S.R. Eddy, R.D. Finn, and E.L. Sonnhammer
  Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
  Nucleic Acids Research 27, January 1 1999, 260-262.
  Also available locally as a PDF file.