[Bioperl-l] GenericResult.pm and HMMERResult.pm question

[Brian Osborne]

Diane,

In the hmmpfam output I have in front of me there's actually no
query_accession or query_length (meaning the length of the entire query, not
the alignment). You should be able to get query_name though. Do you see
these values in your hmmpfam output? Mine is below.

We need Jason's help here...

Brian O.

hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 pfam
Sequence file:            /home/birney/src/wise2/example/road.pep
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query:  roa1_drome

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
SEED                                                    146.1    6.3e-40   2

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
SEED       1/2      33   103 ..     1    77 []    71.2  2.2e-17
SEED       2/2     124   194 ..     1    77 []    75.5  1.1e-18

Alignments of top-scoring domains:
SEED: domain 1 of 2, from 33 to 103: score 71.2, E = 2.2e-17
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lf+g+L + +t+e Lk++F+k G iv++ +++D     + t++s+Gf
  roa1_drome    33    LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGF 74

                   aFVeFeseedAekAlealnG.kelggrklrv<-*
                   +F+++  ++  + A +    +++++gr+++
  roa1_drome    75 GFITYSHSSMIDEAQK--SRpHKIDGRVVEP    103

SEED: domain 2 of 2, from 124 to 194: score 75.5, E = 1.1e-18
                   *->lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGf
                      lfVg L  d +e+ ++d+F++fG iv+i+iv+D     ketgk +Gf
  roa1_drome   124    LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGF 165

                   aFVeFeseedAekAlealnGkelggrklrv<-*
                   aFVeF++++ ++k +     ++l+g+ + v
  roa1_drome   166 AFVEFDDYDPVDKVVL-QKQHQLNGKMVDV    194

//


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Diane Benz (CCGB)
Sent: Friday, March 14, 2003 12:16 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] GenericResult.pm and HMMERResult.pm question

Hello,
I am trying to parse and extract some information from a hmmpfam report
using bioperl. I have a list of fields that I would like to extract, but
I am having problems extracting fields such as the accession number
through methods $result->query_accession(),  $result->query_length() and
others. Should I be able to extract these fields? This is in essence how
I am using bioperl:

use Bio::SearchIO;

.
.
.
my $report = new Bio::SearchIO(-format => 'hmmer',
                                                        -fh         =>
\*filehandle);

while (my $result = $report->next_result) {
  while (my $hit = $result->next_hit) {
      while (my $hsp = $hit->next_hsp) {
           print $result->query_accession();
           print $result->query_length();
       }
  }
}


I would appreciate any suggestions.
Thanks, Diane Benz









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