Scribe: N. Allen

Today's Handouts and Announcements

• Announce: All work must be submitted by Friday morning if you want a grade.

Today's Topics

• Sequence Comparison
  • (continued from Tuesday)
  • AUTOMAT developed by Cantalloube in Paris
  • SALSA (Searching with Assembly of Local Sequence Alignment)
    • Developed by Rognes and Seeberg in Norway
    • Merges extended w-mers using a gaped alignment
      1. Consider fragments as diagonal runs in the alignment table
      2. An extension of an alignment continues the diagonal run to the edges of the table
      3. Merging is equivalent to connecting two fragment extensions with horizontal or vertical runs
      4. Candidates for merging have their score increased by adding another fragment's score and subtracting the penalty for connecting the two
      5. Combining candidate fragments produces longer runs then other tools but may not have any biological significance
    • Slower then BLAST which it's based on but much faster then SSEARCH

• Maximum Likelihood
• (continued from Monday and Tuesday)
• Directly determines tree shape but not exact node values.
• Can later compute probabilities of node values given structure.
• Likelihood calculations can be done for each tree and then maximized to find the maximum likelihood
• If P_ij * PI_j = P_ji * PI_i then the layout is reversible
• If the layout is reversible, the choice of the root does not affect the likelihood estimate
• Motif Searching
  • A motif is a small substring characteristic of the family it comes from
  • Looking for motifs which determine function across many sequences
  • (to be continued Thursday)

Today's Sources

• Sources listed on the CS6104 Student Talks page under Douglas Slotta.
• Sources listed on the CS6104 Student Talks page under Subhag Oak.
• Sources listed on the CS6104 Student Talks page under Chad Wingrave.