In this section, protein sequence pairs will be aligned using Internet servers.

1. Using one of the Web sites listed below and the default conditions provided by the Web site, align the protein sequences for the phage λ and p22 phage repressors. Cut and paste FASTA files of the sequences already available into these sites.
2. Record the resulting percent identity and similarity and briefly describe what each represents.

Internet Sites for Sequence Alignment

The following are Web sites that will perform sequence alignment of two sequences by the dynamic programming algorithm.

1. LALIGN (http://fasta.bioch.virginia.edu/) at the University of Virginia. This program is also available for Mac and PC computers but without a windows/mouse interface. The program finds not just 1, but also n nonoverlapping alignment of two sequences according to the SIM algorithm discussed in the text. In these alignments, the same two residues will never be found together more than once.
2. SIM (http://us.expasy.org/tools/sim-prot.html) uses the same algorithm as the above site.
3. BCM (http://searchlauncher.bcm.tmc.edu/) Baylor College of Medicine Web site offers a variety of methods of sequence alignment. Read the "h" option to see how these programs work. Not all of these programs use dynamic programming as the sole method. LFASTA and BLAST2 search for common words and then align on the basis of these words. The program align is a global alignment program based on the Needleman�Wunsch alignment algorithm instead of the Smith�Waterman local alignment algorithm. Unless dealing with strongly similar sequences of the same length, and alike along their entire lengths, a global alignment will not be useful.