15 Aug 01:04
Re: HOWTO:Graphics/BLAST output
From: N <downloadondemand <at> gmail.com>
Subject: Re: HOWTO:Graphics/BLAST output
Newsgroups: gmane.comp.lang.perl.bio.general
Date: 2008-08-14 23:06:04 GMT
Subject: Re: HOWTO:Graphics/BLAST output
Newsgroups: gmane.comp.lang.perl.bio.general
Date: 2008-08-14 23:06:04 GMT
Hello again!
Followed HOWTO:Graphics and encountered problem.
While parsing blast output i have clearly offending for me part of file. The
problem is that in this hit there are two HSPs, but the second one is in
"not right" strand orientation (Plus/Plus vs. Plus/Minus). How can i tell
bioperl to use only HSPs oriented along with the best-scored HSP? Or better,
althrough not related to this mailing list: How can i tell BLAST to put this
second HSP to a separate hit? What am i doing/thinking wrong?
Attached small png with problem. The second HSP is in white, but it is
biologically without sense, isn't it?
Thanks.
BLASTN 2.2.18 [Mar-02-2008]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|145226209
(471 letters)
Database: ../database/1000
24 sequences; 19,482 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits)
Value
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