[Bioperl-l] Fwd: blast.pm patch

[Robson Francisco de Souza]

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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