Biomedical Engineering Reference
In-Depth Information
The Kestrel implementation of Smith-Waterman supports the use of PAM-10 through PAM-500 and
BLOSUM30 through BLOSUM100 substitution matrices against the SWISS-PROT or NR protein
databases, or a nucleotide search against the dbEST part 1 database. A maximum of 40 alignments
can be e-mailed to the address specified in the query form.
DotLet
The DotLet dot matrix analysis program, available on the Expert Protein Analysis System (ExPASy)
server, is one of the most popular of the Web-based dot matrix analysis programs. As shown in
Figure 8-18
, the program—a Java applet—supports the pairwise analysis of nucleotide or polypeptide
sequences that are pasted into the pop-up input fields accessed by the "input" button. DotLet also
supports a variety of matrices (Blosum30 to Blosum100 and PAM-30 to PAM-250), sliding window
size (1 to 15), and zoom (1:1 to 1:8) through pull-down menus along the top of the screen.
Figure 8-18. DotLet Dot Matrix Analysis Program on the ExPASy Server.
This plot of the
Drosophila melanogaster
SLIT protein, plotted against
itself, illustrates perfect alignment of two polypeptide sequences. At lower
magnification, patterns of repeated protein domains are visible.
