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Home > Problems > Chapter 5
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.
- 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.
- Try to align these proteins by searching for the POA, DIALIGN, and CLUSTALW Web sites and pasting the sequences into the program sequence window.
- 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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