July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Command-Line Tutorial
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175
You can’t increase this number with a command-line switch, and the only
workaround is to cut your query sequence into smaller pieces. This limitation applies
only in ungapped searches (TBLASTX or any search with the setting
-g F).
[blastall] WARNING: [000.000] gi|18463974|gb|AY016024.1|: Reached max 200 HSPs in
BlastSaveCurrentHsp, continuing with this limit
Since there’s only one sequence in the database, look at the first alignment instead of
the summary:
>gi|17104478|gb|AY016020.1| Gallus gallus alpha globin gene cluster,
complete sequence
Length = 103190
Score = 141 bits (302), Expect = 1e-34
Identities = 61/73 (83%), Positives = 66/73 (89%)
Frame = -2 / -3
Query: 25076 ASSDDMTLTSPSMDNSSAELLPGGDSPLNKRITETLLASLSEHERQVILSVPAAQNPEDL 24897
ASSDDMTLTSPSMDNSSAEL+PGGDSPLNKR+TE LLASL EHER+ IL+VPAAQNPEDL
Sbjct: 5289 ASSDDMTLTSPSMDNSSAELIPGGDSPLNKRMTENLLASLLEHEREAILNVPAAQNPEDL 5110
Query: 24896 RMFAR*NHLSTKC 24858
RMFAR* S +C
Sbjct: 5109 RMFAR*EIGSAEC 5071
Note the stop codon (*) near the end of the alignment. The scoring matrices distrib-
uted with BLAST set the score of all stop codon matches to +1. If you want to termi-
nate alignments at stop codons, you have to edit the scoring matrix. This procedure
is described at the end of this chapter.
bl2seq
The previous
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
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.