July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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BLASTX Protocols
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147
NCBI-BLAST parameters
blastall -p blastp -d <db> -i <query> -f 9 -F "m S" -M BLOSUM45 -e 100 -b 10000 -v
10000
WU-BLAST parameters
blastp <db> <query> T=9 wordmask=seg hitdist=60 matrix=BLOSUM50 Q=13 R=1 E=100
B=10000 V=10000
Expected results
Whenever you increase sensitivity, expect a decrease in specificity. These parameters
are very sensitive, so many of the alignments may be chance similarities and of no
biological significance. On the other hand, some biological signals aren’t modeled
well by BLAST statistics and what may appear as a very low score may be of real
interest. Reading a BLAST report containing thousands of alignments isn’t always
entertaining, so if you’re looking for something specific, such as an alignment to a
particular region, you may be able to automate the reading with a BLAST parser.
Optimizations and variations
The probability model of BLAST assumes that amino acid pairings are independent
of their neighbors. But some domains have characteristic signatures. So if your pro-
tein belongs to a family of related proteins, you may be able to find more distant rela-
tives by choosing an algorithm with a position-specific scoring matrix, such as PSI-
BLAST or HMMER. However, if your query is a novel protein, the best you can do is
make your search ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.