Question: Which Bioperl Module Can I Use For Parsing/Mining Blast Output?
0
gravatar for Raghul
7.3 years ago by
Raghul200
Italy
Raghul200 wrote:

Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in Frame=1, Frame=2, etc separately.

I think it is possible using Bioperl. All kind of suggestions are welcome. If somebody has similar bioperl programs, u can post it. So I will get an idea how to start write my own script! I am giving you a portion of blastx output if u want to know more.

THANK YOU raghul

Query= isotig00043|appr-1-p processing domain protein Length=2377

contig0391611122816230- 144 5.6e-34 gi|20178254|sp|Q96XY5|Y2383_SULTO Length=230

Score = 62.4 bits (150), Expect(2) = 2e-016 Identities = 37/123 (30%), Positives = 60/123 (48%), Gaps = 10/123 (8%) Frame = -2

Query 474 KYVFHTVGPMCQKGKLDLRKESKQLKSCVEEVLKLMIKKNCKSICLLAISTGIFNFPLTN 295 KY H VGP+ G KQL+ + K + C+S+ + AIS+GIF +PL
Sbjct 59 KYCIHAVGPIY--GYSGGENAEKQLELTIVNTYKRAEELKCESVSVPAISSGIFGYPLKE 116

perl bioperl blast output parsing • 2.8k views
ADD COMMENTlink modified 7.0 years ago by Yogesh Pandit490 • written 7.3 years ago by Raghul200
2
gravatar for Michael Schubert
7.3 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

http://www.bioperl.org/wiki/HOWTOs

ADD COMMENTlink written 7.3 years ago by Michael Schubert6.9k
1
gravatar for Yogesh Pandit
7.3 years ago by
Yogesh Pandit490
United States
Yogesh Pandit490 wrote:

Link to the SearchIO module from Michael's answer

http://www.bioperl.org/wiki/HOWTO:SearchIO

Similar question was asked in the SEQanswers forum

http://seqanswers.com/forums/showthread.php?t=6484

ADD COMMENTlink written 7.3 years ago by Yogesh Pandit490
0
gravatar for Scott Cain
7.3 years ago by
Scott Cain750
Scott Cain750 wrote:

And, should Michael's excellent suggestion not work out:

http://lists.open-bio.org/mailman/listinfo/bioperl-l

ADD COMMENTlink written 7.3 years ago by Scott Cain750

should there really be a problem that is not easily resolvable with the basic tutorials, the question is welcome here as well ;-)

ADD REPLYlink written 7.3 years ago by Michael Schubert6.9k
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