Biomedical Engineering Reference
In-Depth Information
Up to four sets of scoring matrix, gap penalty, and gap extension penalty combinations can be
specified. The PAM-250 as well as Blosum30 to Blosum80 scoring matrices are available. Output,
which consists of the posterior probability for each scoring matrix/gap penalty/gap extension
combination, is sent to the e-mail address entered on the form. A separate output is provided for
each matrix-gap entry specified.
Polypeptide Pattern Matching
BLASTP
Protein-Protein BLAST (BLASTP) shares many of the features and options of BLASTN, with a focus on
polypeptide sequences instead of nucleotide sequences. The BLASTP interface is similar to the
interface used with BLASTN, as illustrated in
Figure 8-16
. The major differences are in the databases
available and in the advanced options available in BLASTP. For example, the peptide parallels to the
nucleotide sequence databases are available to BLASTP, including "nr" (non-redundant GenBank CDS
translations, PDB, SWISS-PROT, PIR, and PRF), "swissprot" (SWISS-PROT protein sequence
database), and "month" (the GenBank CDS translation, PDB, SWISS-PROT, PIR, and PRF data
released in the last 30 days).
Figure 8-16. NCBI's Protein-Protein BLAST (BLASTP) Web Interface.
