[Bioperl-l] Blast returns result, but does not return hits

Chris Fields cjfields at uiuc.edu
Wed Feb 22 14:45:54 EST 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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