[Bioperl-l] Blast returns result, but does not return hits
Raghunath Verabelli
iamvela at yahoo.com
Wed Feb 22 17:21:59 UTC 2006
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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