Homology searching

• BLAST suite

  • BLASTN, BLASTX, TBLASTX, PSI-BLAST
  • Altschul et al. (1990), JMB, 215, 403-410.
  • http://www.ncbi.nlm.nih.gov/BLAST

• FASTA suite

  • FASTA, TFASTA
  • Pearson and Lipman (1988), PNAS, 85, 2444-2448.

• HMM-based searching

  • SAM (UCSC group)
    • http://www.cse.ucsc.edu/research/compbio/sam.html
  • HMMER, Sean Eddy
    • http://hmmer.wustl.edu/

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