[Bioperl-l] Bio::SearchIO::hmmer

shalabh sharma shalabh.sharma7 at gmail.com
Wed Sep 1 16:56:35 EDT 2010


Hi ,
     I am trying to parse hmmsearch report (from HMMER3). I am using the
script mentioned here:
http://search.cpan.org/~birney/bioperl-1.2.3/Bio/SearchIO/hmmer.pm

I am not getting anything but this "amoA_10genes_align.fasta.2  [M=247] for
HMM" as the output, i am not even getting any error.
I am attaching the hmmsearch report (just a test report) which i tried to
test against the parser.

I would really appreciate if anyone can help me out.

Thanks
Shalabh Sharma
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# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  amoA_10genes.hmm
# target sequence database:        test.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       amoA_10genes_align.fasta.2  [M=247]
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                   Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                   -----------
    1.6e-72  231.1   5.1    1.7e-72  231.0   3.5    1.0  1  gi|63021979|gb|AAY26564.1| AmoA [uncultured beta proteobacte
    1.6e-72  231.1   5.1    1.7e-72  231.0   3.5    1.0  1  gi|63021981|gb|AAY26565.1| AmoA [uncultured beta proteobacte


Domain annotation for each sequence (and alignments):
>> gi|63021979|gb|AAY26564.1|  AmoA [uncultured beta proteobacterium]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0   3.5   1.7e-72   1.7e-72     113     245 ..       1     144 [.       1     146 [. 0.95

  Alignments for each domain:
  == domain 1    score: 231.0 bits;  conditional E-value: 1.7e-72
  amoA_10genes_align.fasta.2 113 lyPinfvlpsvllPsallldavlalkrnklvtalvGGglfGlllypgnwplfgavhlllvaegvllsladyvgfkyvrtgtPe 195
                                 +yPinfv+ps+++P+al++d+v++l+rn+++talvGGg+fGll+ypgnwp+fg++hl+lvaegvllslady+gf+yvrtgtPe
  gi|63021979|gb|AAY26564.1|   1 HYPINFVFPSTMIPGALIMDTVMLLTRNWMITALVGGGAFGLLFYPGNWPIFGPTHLPLVAEGVLLSLADYTGFLYVRTGTPE 83 
                                 8********************************************************************************** PP

  amoA_10genes_align.fasta.2 196 yvrliekgslrtfgkstvaiaaffsafvsvlmfavwaylgklyskaf...........kkd 245
                                 yvrlie+gslrtfg++t++iaaffsafvs+lmf+vw+y+gkly++af           +k+
  gi|63021979|gb|AAY26564.1|  84 YVRLIEQGSLRTFGGHTTVIAAFFSAFVSMLMFCVWWYFGKLYCTAFyyvkgprgrvtMKN 144
                                 **********************************************966666666655555 PP

>> gi|63021981|gb|AAY26565.1|  AmoA [uncultured beta proteobacterium]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0   3.5   1.7e-72   1.7e-72     113     245 ..       1     144 [.       1     146 [. 0.95

  Alignments for each domain:
  == domain 1    score: 231.0 bits;  conditional E-value: 1.7e-72
  amoA_10genes_align.fasta.2 113 lyPinfvlpsvllPsallldavlalkrnklvtalvGGglfGlllypgnwplfgavhlllvaegvllsladyvgfkyvrtgtPe 195
                                 +yPinfv+ps+++P+al++d+v++l+rn+++talvGGg+fGll+ypgnwp+fg++hl+lvaegvllslady+gf+yvrtgtPe
  gi|63021981|gb|AAY26565.1|   1 HYPINFVFPSTMIPGALIMDTVMLLTRNWMITALVGGGAFGLLFYPGNWPIFGPTHLPLVAEGVLLSLADYTGFLYVRTGTPE 83 
                                 8********************************************************************************** PP

  amoA_10genes_align.fasta.2 196 yvrliekgslrtfgkstvaiaaffsafvsvlmfavwaylgklyskaf...........kkd 245
                                 yvrlie+gslrtfg++t++iaaffsafvs+lmf+vw+y+gkly++af           +k+
  gi|63021981|gb|AAY26565.1|  84 YVRLIEQGSLRTFGGHTTVIAAFFSAFVSMLMFCVWWYFGKLYCTAFyyvkgprgrvtMKN 144
                                 **********************************************966666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (247 nodes)
Target sequences:                          2  (300 residues)
Passed MSV filter:                         2  (1); expected 0.0 (0.02)
Passed bias filter:                        2  (1); expected 0.0 (0.02)
Passed Vit filter:                         2  (1); expected 0.0 (0.001)
Passed Fwd filter:                         2  (1); expected 0.0 (1e-05)
Initial search space (Z):                  2  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.08
# Mc/sec: 0.93
//


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