Which Bioperl Module Can I Use For Parsing/Mining Blast Output?
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12.6 years ago
Raghul ▴ 200

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

blast output parsing bioperl perl • 4.1k views
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12.6 years ago
Yogesh Pandit ▴ 520

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

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12.6 years ago
Scott Cain ▴ 770

And, should Michael's excellent suggestion not work out: http://lists.open-bio.org/mailman/listinfo/bioperl-l

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

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