Biomedical Engineering Reference
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conserved region of a sequence of motif. A PSSM is used in the scoring of multiple alignments with
sequences. A PSSM plots the probability score for the occurrence of each amino acid along the length
of a motif.
PSI-BLAST, which is based on the BLAST algorithm, is enhanced to be more sensitive than BLASTP.
This sensitivity comes from the use of a profile of the position-specific scores for every position in the
alignment that is constructed from a multiple alignment of the highest-scoring hits in the initial
BLAST search. The profile or matrix created by PSI-BLAST can be formatted, saved, and then pasted
into the PSSM field of BLASTP.
A feature recently added to BLASTP is the ability to specify a PHI pattern, which is used by PHI-
BLAST (Pattern Hit Initiated BLAST) to search for similarities that are presumably also homologues.
PHI-BLAST, which expects as input a protein query sequence and a pattern contained in that
sequence, searches the current database for other protein sequences that also contain the input
pattern and have significant similarity to the query sequence in the vicinity of the pattern
occurrences. PHI-BLAST filters out cases where the pattern occurrence is probably random and not
indicative of homology.
Smith-Waterman
The Smith-Waterman dynamic programming algorithm is available on the UCSC Kestrel Server, which
is an experimental, high-performance, 512-processor system. As shown in Figure 8-17 , compared to
the BLASTP interface with its array of options, the interface presented by the Kestrel Server appears
somewhat limited. The parameters are simply costs to open and extend gaps, the substitution
matrix, the database to search, and the number of alignments to report.
Figure 8-17. Smith-Waterman on the High-Performance UCSC Kestrel
Server.
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