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2. Go to the BAliBASE Web site and retrieve the SwissProt accession numbers of the 1csy (SH2) group of proteins that align in the 20-40% identity, reference 1 range.
  1. Retrieve these sequences from SwissProt and, using a simple text editor, place them in the FASTA msa format. Note that the BAliBASE alignments are based on known structural alignments and therefore are a test of the ability of msa programs to provide an msa that is structurally correct.
  2. Try to align these proteins by searching for the POA, DIALIGN, and CLUSTALW Web sites and pasting the sequences into the program sequence window.
  3. Compare the alignments to the correct ones on the BAliBASE site and note which program, if any, does the best job.


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