[Bioperl-l] Blast returns result, but does not return hits
Chris Fields
cjfields at uiuc.edu
Wed Feb 22 19:45:54 UTC 2006
Upgrade bioperl from CVS using nmake.
Installation instructions for using nmake:
http://www.bioperl.org/wiki/INSTALL.WIN#Beyond_the_Core
You can download a tarball using anonymous CVS (link at bottom):
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
or use CVS directly:
http://www.bioperl.org/wiki/Using_CVS
Then make sure to grab the last SearchIO::last bugfix, which is not in CVS
yet:
http://bugzilla.bioperl.org/show_bug.cgi?id=1934
Replace the blast.pm in \site\lib\Bio\SearchIO in your Perl directory.
Does that fix it?
Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Raghunath Verabelli
> Sent: Wednesday, February 22, 2006 11:22 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Blast returns result, but does not return hits
>
> Hi All:
>
> I am new to Perl/BioPerl world.
>
> I am debugging a program that used to work fine
> before.
> Blast works fine and returns results, but I am unale
> to get any hits from the results.
>
> Here is the relevant code:
>
> $blastObj = new Bio::SearchIO (-file=>$resultsFile,
> -format=>'blast');
> while (my $result = $blastObj->next_result()) {
> while (my $bioPerlHit = $result->next_hit()) {
> .......
>
>
> The first while condition returns true, but the second
> while condition returns false. So looks like there is
> some result, but it is unable to identify the hits in
> the result. I printed the $result (pasted below).
>
> Any ideas/comments to resolve this? Thanks in advance.
>
> I am using Perl 5.8.7, BioPerl 1.2.3, Apache 1.3.34 on
> Windows XP platform.
>
> Like I said before, this application was running fine
> on a different windows machine with similar
> environment,so looks like there is some change in the
> products/versions that is causing the problem.
>
> thanks again,
> Raghu
>
>
>
>
> Blast result (i can send complete result if you need
> it):
>
> <p><!--
> QBlastInfoBegin
> Status=READY
> QBlastInfoEnd
> --><p><PRE>
> BLASTP 2.2.13 [Nov-27-2005]
> Reference: Altschul, Stephen F., Thomas L. Madden,
> Alejandro A. Schäffer,
> 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.
>
> RID: 1140573059-19990-140117828872.BLASTQ1
>
>
> Database: All non-redundant GenBank CDS
> translations+PDB+SwissProt+PIR+PRF excluding
> environmental samples
> 3,297,000 sequences; 1,129,354,045 total
> letters
> Query=
> Length=360
>
>
>
> Score E
> Sequences producing significant alignments:
> (Bits) Value
>
> ref|XP_534770.2| PREDICTED: similar to
> Mitogen-activated prot... 739 0.0
> gb|AAX36107.1| mitogen-activated protein kinase 1
> [synthetic con 739 0.0
> pdb|1WZY|A Chain A, Crystal Structure Of Human Erk2
> Complexed... 739 0.0
> pdb|1TVO|A Chain A, The Structure Of Erk2 In Complex
> With A S... 739 0.0
> ref|NP_786987.1| mitogen-activated protein kinase 1
> [Bos taur... 739 0.0
> emb|CAA77752.1| 41kD protein kinase [Homo sapiens]
> >prf||1813... 738 0.0
> gb|AAQ02541.1| mitogen-activated protein kinase 1
> [synthetic con 736 0.0
> gb|AAH99905.1| Mitogen-activated protein kinase 1
> [Homo sapiens] 735 0.0
> emb|CAI29602.1| hypothetical protein [Pongo pygmaeus]
> 734 0.0
> gb|AAH58258.1| Mitogen activated protein kinase 1
> [Mus muscul... 731 0.0
> pdb|4ERK| The Complex Structure Of The Map Kinase
> Erk2OLOMOU... 731 0.0
> pdb|1GOL| Coordinates Of Rat Map Kinase Erk2 With An
> Arginin... 730 0.0
> ref|XP_860750.1| PREDICTED: similar to
> Mitogen-activated prot... 729 0.0
> gb|AAK56503.1| extracellular signal-regulated kinase
> 2 [Gallu... 726 0.0
> ref|XP_860716.1| PREDICTED: similar to
> Mitogen-activated prot... 726 0.0
> pdb|2ERK| Phosphorylated Map Kinase Erk2
> 726 0.0
> pdb|1PME| Structure Of Penta Mutant Human Erk2 Map
> Kinase Co... 725 0.0
> ref|XP_860682.1| PREDICTED: similar to
> Mitogen-activated prot... 720 0.0
> ref|XP_860651.1| PREDICTED: similar to
> Mitogen-activated prot... 720 0.0
> emb|CAA77753.1| 40kDa protein kinase [Homo sapiens]
> >prf||181... 717 0.0
> ref|NP_001017127.1| mitogen-activated protein kinase
> 1 [Xenopus 715 0.0
> dbj|BAE28679.1| unnamed protein product [Mus
> musculus] 713 0.0
> emb|CAA42482.1| MAP kinase [Xenopus laevis]
> >gb|AAH60748.1| M... 711 0.0
> sp|P26696|MK01_XENLA Mitogen-activated protein kinase
> 1 (Myel... 711 0.0
> gb|AAH76730.1| Xp42 protein [Xenopus laevis]
> 706 0.0
> gb|AAH65868.1| Mitogen-activated protein kinase 1
> [Danio rerio] 696 0.0
> dbj|BAD23843.1| extracellular signal regulated
> protein kinase... 694 0.0
> ref|NP_878308.2| mitogen-activated protein kinase 1
> [Danio re... 694 0.0
> emb|CAG07778.1| unnamed protein product [Tetraodon
> nigroviridis] 692 0.0
> dbj|BAB11813.1| ERK2 [Danio rerio]
> 689 0.0
> gb|AAY57805.1| extracellular signal-regulated kinase
> 2 [Danio re 687 0.0
> gb|AAH45505.1| Mitogen-activated protein kinase 3
> [Danio reri... 654 0.0
> dbj|BAB11812.1| ERK1 [Danio rerio]
> 654 0.0
> ref|XP_609884.2| PREDICTED: similar to mitogen
> activated prot... 653 0.0
> dbj|BAD23842.1| extracellular signal regulated
> protein kinase... 650 0.0
> gb|AAH29712.1| Mitogen activated protein kinase 3
> [Mus muscul... 644 0.0
> ref|XP_885698.1| PREDICTED: similar to mitogen
> activated prot... 644 0.0
> gb|AAA20009.1| microtubule-associated protein-2
> kinase 643 0.0
> emb|CAA46318.1| MAP kinase [Rattus norvegicus]
> >ref|NP_059043... 641 0.0
> gb|AAH13992.1| Mitogen-activated protein kinase 3
> [Homo sapie... 641 0.0
> gb|AAQ02422.1| mitogen-activated protein kinase 3
> [synthetic ... 641 0.0
> gb|AAA41123.1| extracellular signal-regulated kinase
> 1 640 0.0
> ref|XP_854045.1| PREDICTED: similar to mitogen
> activated prot... 640 0.0
> gb|AAA63486.1| extracellular-signal-regulated kinase
> 1 [Rattus n 640 0.0
> emb|CAG02655.1| unnamed protein product [Tetraodon
> nigroviridis] 640 0.0
> emb|CAA42744.1| protein serine/threonine kinase [Homo
> sapiens... 639 0.0
> gb|AAA36142.1| kinase 1
> 639 0.0
> emb|CAA77754.1| 44kDa protein kinase [Homo sapiens]
> >prf||181... 639 0.0
> ref|XP_885840.1| PREDICTED: similar to mitogen
> activated prot... 632 5e-180
> ref|XP_885818.1| PREDICTED: similar to mitogen
> activated prot... 630 3e-179
> ref|XP_860621.1| PREDICTED: similar to
> Mitogen-activated prot... 627 2e-178
> gb|AAF71666.1| extracellular signal-regulated kinase
> 1b [Rattus 627 2e-178
> ref|XP_393029.1| PREDICTED: similar to MAP kinase
> [Apis mellifer 621 1e-176
> gb|AAA83210.1| MAP kinase
> 619 4e-176
> dbj|BAE46741.1| Extracellular regulated MAP kinase
> [Bombyx mori] 618 1e-175
> gb|AAH13754.1| Mapk3 protein [Mus musculus]
> 612 9e-174
> dbj|BAE06412.1| mitogen-activated protein kinase
> [Ciona intestin 607 2e-172
> dbj|BAE33167.1| unnamed protein product [Mus
> musculus] 600 3e-170
> gb|AAN46679.1| MAP kinase [Strongylocentrotus
> purpuratus] >re... 598 1e-169
> dbj|BAC02940.1| mitogen-activated protein kinase
> [Halocynthia ro 592 6e-168
> gb|AAL48618.1| RE08694p [Drosophila melanogaster]
> >gb|EAA4631... 590 2e-167
> emb|CAD97888.1| hypothetical protein [Homo sapiens]
> 589 5e-167
> emb|CAD60453.1| extracellular signal-regulated
> protein kinase... 589 5e-167
> emb|CAD56894.1| mitogen-activated protein kinase 1
> [Meloidogyne 589 6e-167
> ref|XP_536917.2| PREDICTED: similar to mitogen
> activated prot... 588 1e-166
> gb|AAN40736.1| mitogen-activated protein kinase
> [Paralichthys ol 586 4e-166
> emb|CAE73725.1| Hypothetical protein CBG21247
> [Caenorhabditis br 583 3e-165
> emb|CAA87057.1| Hypothetical protein F43C1.2a
> [Caenorhabditis... 581 2e-164
> gb|AAA18956.1| Sur-1 MAP kinase
> 581 2e-164
> emb|CAB60996.1| Hypothetical protein F43C1.2b
> [Caenorhabditis... 581 2e-164
> gb|AAK52329.1| extracellular signal-related kinase 1b
> [Homo sapi 580 4e-164
> ref|XP_885794.1| PREDICTED: similar to mitogen
> activated prot... 553 4e-156
> ref|XP_868146.1| PREDICTED: similar to mitogen
> activated prot... 548 2e-154
> gb|AAK52330.1| extracellular signal-related kinase 1c
> [Homo sapi 546 4e-154
> dbj|BAA22620.1| ERK2 [Mus musculus]
> 544 2e-153
> ref|XP_510921.1| PREDICTED: mitogen-activated protein
> kinase 3 [ 529 8e-149
> gb|AAT02418.1| MAP kinase [Schistosoma japonicum]
> 496 7e-139
> emb|CAJ44437.1| MAP kinase [Echinococcus
> multilocularis] 491 1e-137
> ref|XP_885774.1| PREDICTED: similar to mitogen
> activated prot... 444 3e-123
> gb|EAA14714.3| ENSANGP00000016639 [Anopheles gambiae
> str. PES... 431 2e-119
> gb|AAZ38881.1| extracellular regulated kinase
> [Littorina littore 431 2e-119
> emb|CAD60723.1| unnamed protein product [Podospora
> anserina] 411 2e-113
> gb|AAK25816.1| MAP kinase [Neurospora crassa]
> >ref|XP_959713.... 411 2e-113
> gb|EAL89122.1| MAP kinase (FUS3/KSS1), putative
> [Aspergillus ... 409 1e-112
> gb|EAA74589.1| hypothetical protein FG06385.1
> [Gibberella zea... 409 1e-112
> ref|XP_504312.1| hypothetical protein [Yarrowia
> lipolytica] >... 408 2e-112
> gb|AAG01162.1| mitogen-activated protein kinase
> [Fusarium oxy... 408 2e-112
> gb|AAS20192.1| AMK1 [Alternaria brassicicola]
> >gb|AAK52840.1|... 408 2e-112
> dbj|BAE57584.1| unnamed protein product [Aspergillus
> oryzae] 408 2e-112
> dbj|BAD42855.1| mitogen-activated protein kinase
> [Bipolaris oryz 407 3e-112
> gb|AAD50496.1| mitogen activated protein kinase
> [Colletotrichum 407 3e-112
> gb|AAF05913.1| mitogen-activated protein kinase
> [Cochliobolus he 407 3e-112
> gb|AAM89501.1| mitogen-activated protein kinase
> [Leptosphaeria m 407 3e-112
> dbj|BAB21569.1| mitogen-activated protein kinase
> [Glomerella cin 407 3e-112
> gb|AAB72017.1| mitogen-activated protein kinase
> [Nectria haem... 407 3e-112
> emb|CAC36428.1| mitogen activated protein kinase
> [Gibberella fuj 406 6e-112
> ref|XP_364720.1| hypothetical protein MG09565.4
> [Magnaporthe gri 406 6e-112
> gb|AAG23132.1| MAP kinase [Botryotinia fuckeliana]
> 406 6e-112
> gb|AAO63561.1| mitogen activated protein kinase
> [Verticillium fu 406 8e-112
> dbj|BAE53432.1| MAP kinase Pmk1 [Hypocrea lixii]
> 405 1e-111
>
> ALIGNMENTS
> >ref|XP_534770.2| PREDICTED: similar to
> Mitogen-activated protein kinase 1 (Extracellular
> signal-regulated kinase 2) (ERK-2) (Mitogen-activated
> protein kinase 2) (MAP kinase 2) (MAPK 2) (p42-MAPK)
> (ERT1)
> isoform 1 [Canis familiaris]
> ref|NP_620407.1| mitogen-activated protein kinase 1
> [Homo sapiens]
> ref|NP_002736.3| mitogen-activated protein kinase 1
> [Homo sapiens]
> gb|AAH17832.1| Mitogen-activated protein kinase 1
> [Homo sapiens]
> sp|P28482|MK01_HUMAN Mitogen-activated protein kinase
> 1 (Extracellular signal-regulated
> kinase 2) (ERK-2) (Mitogen-activated protein kinase 2)
>
> (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1)
> gb|AAA58459.1| protein kinase 2
> Length=360
>
> Score = 739 bits (1909), Expect = 0.0
> Identities = 360/360 (100%), Positives = 360/360
> (100%), Gaps = 0/360 (0%)
>
> Query 1
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 60
>
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> Sbjct 1
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 60
>
> Query 61
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> 120
>
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> Sbjct 61
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> 120
>
> Query 121
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> 180
>
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> Sbjct 121
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> 180
>
> Query 181
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> 240
>
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> Sbjct 181
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> 240
>
> Query 241
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> 300
>
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> Sbjct 241
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> 300
>
> Query 301
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> 360
>
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> Sbjct 301
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> 360
>
>
> >gb|AAX36107.1| mitogen-activated protein kinase 1
> [synthetic construct]
> Length=361
>
> Score = 739 bits (1909), Expect = 0.0
> Identities = 360/360 (100%), Positives = 360/360
> (100%), Gaps = 0/360 (0%)
>
> Query 1
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 60
>
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> Sbjct 1
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 60
>
> Query 61
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> 120
>
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> Sbjct 61
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> 120
>
> Query 121
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> 180
>
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> Sbjct 121
> LSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDH
> 180
>
> Query 181
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> 240
>
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> Sbjct 181
> TGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHI
> 240
>
> Query 241
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> 300
>
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> Sbjct 241
> LGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHK
> 300
>
> Query 301
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> 360
>
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> Sbjct 301
> RIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
> 360
>
>
> >pdb|1WZY|A Chain A, Crystal Structure Of Human Erk2
> Complexed With A Pyrazolopyridazine
> Derivative
> Length=368
>
> Score = 739 bits (1909), Expect = 0.0
> Identities = 360/360 (100%), Positives = 360/360
> (100%), Gaps = 0/360 (0%)
>
> Query 1
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 60
>
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> Sbjct 9
> MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFE
> 68
>
> Query 61
> HQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQH
> 120
>
>
>
>
>
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