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

Raghunath Verabelli iamvela at yahoo.com
Wed Feb 22 12:21:59 EST 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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