Scribe: Chad Wingrave

Today's Handouts and Announcements

• Sample BLAST Search Results handout
• Photocopy of "Sequence Comparison and Database Search" pg. 88 S&M
• Dr. Alscher suggested BIOL2104 Cell and Molecular Biology for those interested in more of the biology of bioinformatics
• We choose the subjects we were to work on

Today's Topics

• PsiBlast (Position Specific Iterated BLAST)
  Create a table from all the relevant BLAST results scoring the significance of an amino at a certain position. Use this to search in the future. This focuses on finding functional domains.

• Fasta (see handout)
  • Find all ktuples in s and index
  • Calculate the offset for each sequence
  • Sum offsets in table and choose the largest
  • Align and find regions
  • Take 5 best and rescore w/PAM matrix
  • Take best and look for best local alignment

Today's Sources

• Setubal and Meidanis: Chapter 3.