July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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TBLASTX Protocols
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155
tblastn <est_db> <protein> wordmask=seg W=4 T=20 B=10000 V=10000
tblastn <est_db> <protein> wordmask=seg W=4 T=99 B=10000 V=10000
Expected results
Our seeding parameters are on the insensitive side, so if you don’t find what you’re
looking for, the first parameter to change is T (
-f in NCBI-BLAST). Drop it by one or
two points at a time because the search takes longer with each decrement.
Sequencing errors, especially insertions and deletions, may terminate extension. This
can lead to multiple HSPs or possibly the loss of smaller HSPs. Check the coordi-
nates of the alignments, and if large regions are missing, they may correspond to out-
of-frame coding sequences. They may also be UTRs in a transcript or introns in
genomic sequence. Reducing the search space to increase sensitivity enables you to
recover shorter HSPs; bl2seq is convenient for this task.
Optimizations and variations
If you’re looking for near identities, you can make this search much faster. See the
section “Super-Fast BLASTX” for parameters. Because the query and database
sequences are all short, you can’t optimize this search with a serial strategy.
TBLASTX Protocols
As discussed in Chapter 2, coding sequences evolve slowly compared to surrounding
DNA. This makes TBLASTX a powerful gene-prediction ...
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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.