Biomedical Engineering Reference
In-Depth Information
A feature in the basic BLASTP search is the "Do CD-Search" option, which is checked to compare
protein sequences to the conserved domain (CD) database maintained by NCBI. The "Do CD-Search"
option may be used to identify the conserved domains (modules with distinct evolutionary origin and
function) present in a protein sequence.
Advanced options include the ability to specify a substitution matrix and gap costs. The substitution
matrix is used to assign a score for aligning residue pairs, and should reflect the types of sequences
being searched. The default matrix is BLOSUM62, which assigns a probability score for each position
in an alignment that is based on the frequency with which that substitution is known to occur among
related proteins. The "Gap Costs" field allows the penalties to be specified for opening and extending
a gap. Increasing the gap costs results in alignments with fewer gaps.
The PSSM field holds the matrix automatically computed by PSI-BLAST (Position-Specific Iterative
BLAST). A Position-Specific Scoring Matrix (PSSM) is a matrix of scores representing a locally
