[Bioperl-l] Fwd: blast.pm patch

[Chris Fields]

Robson, 

Any chance you could check this against SVN?  We haven't used the CVS tree for a few years (had a number of releases along the way as well).

Not sure about bioperl-bugs, we have bugzilla still running though:

http://bugzilla.open-bio.org/

chris


On Dec 18, 2009, at 12:07 PM, Robson Francisco de Souza wrote:

> Hi,
> 
> I've been dealing with an apparent bug in the output of NCBI's BLAST
> programs (blastall, blastpgp) which sometimes produces output like the
> one below.
> I think I've managed to produce a work around for Bioperl blast.pm
> parser and would like to contribute it to Bioperl.
> The fix is based on blast.pm from the CVS tree (downloaded some months
> ago...) and is attached to this message.
> Best,
> Robson
> 
> PS: what happened to the bioperl-bugs mailing list? It does not seem
> to be working...
> 
>> gi|156552846|ref|XP_001600053.1| PREDICTED: similar to conserved
>           hypothetical protein [Nasonia vitripennis]
>          Length = 1774
> 
>  Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
>  Identities = 85/393 (21%), Positives = 175/393 (44%), Gaps = 28/393 (7%)
> 
> Query: 0   -
> 
> Sbjct: 328 P                                                            328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 0
> 
> Sbjct: 328                                                              328
> 
> Query: 612 VPPPPGSGIPMPPGGGFFGMKTKLP-----KLPELKATKDTKKIHIAG             654
>            P PP +   + P       KTK+      K+P  K         +
> Sbjct: 329 TPEPPNNSAKLLPQQEIPTPKTKMKTINWNKIPNHKVIGKRNIWSLVA             376
> 
> Query: 655 DKINNKDIEGTGWMSILEENAEKMSKIFDKN-LFENNFQKKETRDAPSQEKENVPTLVSF 713
>           ++  N  +    W  +     +++  +   N    NN       D   +E    PT ++
> Sbjct: 377 NEHQNSPMADLDWAEMEGLFCQQVPPMIPANTTCSNNLGNGVDTDKRRRE----PTEIAL 432
> 
> Query: 714 LDSKTSYQLALLLGFLKKNEREIRKHVIDLNEKELQKQTIHSLKDLCPEEDKFKEIESFV 773
>           LD K S  + + L   + +  +I + + D    ++  + +  L  + PE D+ + ++SF
> Sbjct: 433 LDGKRSLNVNIFLKQFRSSNEDIIQLIKDGGHDDIGAEKLRGLLKILPEVDELEMLKSF- 491
> 
> Query: 774 QKGDGYLEQLEPGDKLFYAMKDIPRLKQRFTAWSSQIYFEGSVISVEPDIESLNRACKNI 833
>              DG   +L   +K F  +  +P  K R      +  F  ++  +EP I S+  A +++
> Sbjct: 492 ---DGDKLKLGNAEKFFLQLIQVPNYKLRIECMLLKEEFAANMSYLEPSINSMILAGEDL 548
> 
> Query: 834 VQCKSLQRLMTLIVLLVNFLNKAKTDKDRVYGFKLNFLTKLGDIKSSSDPNRSMMNYLCE 893
>           +  KSLQ ++ ++++  NFLN      +   G KL+ L KL +I++    N+  MN L
> Sbjct: 549 MTNKSLQEVLYMVLVAGNFLNSGGYAGN-AAGVKLSSLQKLTEIRA----NKPGMN-LIH 602
> 
> Query: 894 FLLAKDDKLIPELLKELK--DYAEVGSRIELPELKKEIGKLNESLKVIQTELEFYKKEQK 951
>           ++  + ++   +LL   +  +  +  ++  + +L  E   L+  +K I+++++    E
> Sbjct: 603 YVAMQAERKRKDLLNFARGMNALDSATKTTVEQLTNEFNALDTRIKKIRSQIQLPTTEA- 661
> 
> Query: 952 FINDKFPKQLDEFYQYAKSEMQKINKAQEKLEKILKEVAKFFGE 995
>                  +Q+ +F Q A+ EM ++ +  E+L+ + + +A+FF E
> Sbjct: 662 ----DIQEQMAQFLQMAEQEMSQLKRDMEELDGVRRTLAEFFCE 701
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