Searching Methods

• FASTA

  • Fast : lookup table to find identities
  • Sensitive : DP to look at the best matches
  • Protein or DNA

• BLAST

  • Very fast : n-tuple method
  • Limited sensitivity
  • Protein or DNA

• PSI-BLAST

  • Fast : n-tuple method
  • Extremely sensitive : iterative searching
  • Protein only

Notes: