Scribe: C. Wingrave

Today's Handouts and Announcements

• SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments: Rognes, Seeberg
• Issues in searching molecular sequence databases: Altschul, Boguski, Gish, Wootton
• Identification of Common Molecular Subsequences: Smith, Waterman
• Parametric and Ensemble Sequence Alignment Algorithms: Waterman
• Automat and BLAST: comparison of two protein sequence similarity search programs: Cantalloube, Labesse, Chomilier, Nahum, Cho, Chams, Achour, Lachgar, Mbika, Issing, Mornon, Bizzini, Zagury, Zagury
• Improved tools for biological sequence comparison: Pearson, Lipman
• Rapid and Sensitive Protein Similarity Searches: Lipman, Pearson
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs: Altschul, Madden, Schaffer, Zhang, Zhang, Miller, Lipman

Today's Topics

• Double Digest Problem (DDP) - see Waterman's book for details
• Interval Graph - can be used to represent the hybridization of probes to the cDNA clone libraries; vertices are fragments and edges are probes
• Consecuative Ones Problem (C1P) - given the matrix of the probe to fragment hybridization, can we find a permutation where all the ones are consecuative

Today's Sources

• Setubal and Meidanis: Chapter 5.