[Bioperl-l] hmmer3.pm question re query and hit coordinates

Peng Zhou zhoupenggeni at gmail.com
Wed Jul 11 13:45:00 EDT 2012


Hello guys,

Just a follow-up, it seems to me the bioperl-live version is still having 
the same problem - calling hit "query" while query sequence "hit". I also 
looked into the test script written for hmmer3 (
bioperl-live/t/SearchIO/hmmer.t), and it doesn't deal with the alignment 
part - I guess that's why this bug was not discovered.

To be simple, here's an output of hmmsearch v3.0:
# 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:                 
 /project/youngn/zhoup/Scripts/spada/profile/21_all.hmm
# target sequence database:       
 /project/youngn/zhoup/Data/misc3/spada/Athaliana/01_genome/12_refseq_orf.fa
# output directed to file:         
/project/youngn/zhoup/Data/misc3/spada/Athaliana/11_hmmSearchX/01_raw.txt
# number of worker threads:        4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CRP0000  [M=75]
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
    ------- ------ -----    ------- ------ -----   ---- --  --------       
          -----------
    5.5e-25   95.0  14.4    5.7e-25   95.0  10.0    1.0  1 
 Chr2_540228_540404_+     

Domain annotation for each sequence (and alignments):
>> Chr2_540228_540404_+  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to 
   envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- ------- 
   ------- -------    ----
   1 !   95.0  10.0   3.6e-30   5.7e-25      20      74 ..       4      59 
.]       1      59 [] 0.95

  Alignments for each domain:
  == domain 1    score: 95.0 bits;  conditional E-value: 3.6e-30
               CRP0000 20 
tegpkvaeartCesqShkFkGpCvsdtnCasvCrtEgfpgGecrg.rrrCfCtkpc 74
                          ++gp+++eartCes+Sh+FkGpCvs +nCa+vC++Egf gG+crg 
rrrC+Ct++c
  Chr2_540228_540404_+  4 
GMGPVTVEARTCESKSHRFKGPCVSTHNCANVCHNEGFGGGKCRGfRRRCYCTRHC 59
                          
568899***99********************************************* PP

And here is a dump of the parsed HSP object:
$VAR1 = bless( {
                 'VERBOSE' => 0,
                 'IDENTICAL' => 0,
                 'RANK' => 1,
                 'STRANDED' => 'NONE',
                 'EVALUE' => '3.6e-30',
                 'HSP_LENGTH' => 56,
                 'ALGORITHM' => 'HMMSEARCH'
                 'SCORE' => '95.0',
                 'GAP_SYMBOL' => '-',
                 'CONSERVED' => 0,
                 
                 'HIT_NAME' => 'Chr2_540228_540404_+',
                 'HIT_DESC' => '',
                 'HIT_START' => '20',
                 'HIT_END' => '74',
                 'HIT_LENGTH' => 56,
                 'HIT_SEQ' => 
'tegpkvaeartCesqShkFkGpCvsdtnCasvCrtEgfpgGecrg-rrrCfCtkpc',
                 'HIT_FRAME' => 0,
                 
                 'QUERY_NAME' => 'CRP0000',
                 'QUERY_DESC' => undef,
                 'QUERY_START' => '4',
                 'QUERY_END' => '59',
                 'QUERY_LENGTH' => '75',
                 'QUERY_FRAME' => 0,
                 'QUERY_SEQ' => 
'GMGPVTVEARTCESKSHRFKGPCVSTHNCANVCHNEGFGGGKCRGfRRRCYCTRHC',
                 
                 'HOMOLOGY_SEQ' => '++gp+++eartCes+Sh+FkGpCvs +nCa+vC++Egf 
gG+crg rrrC+Ct++c',
               }, 'Bio::Search::HSP::HMMERHSP' );

Clearly, the "HIT_START", "HIT_END", "HIT_SEQ" should actually be exchanged 
with "QUERY_START", "QUERY_END" and "QUERY_SEQ" values.

Thanks,

Peng,

On Tuesday, July 19, 2011 11:23:20 PM UTC-5, Givan, Scott A. wrote:
>
> I'll try the bioperl-live version. Thanks guys. 
>
> Scott Givan
> 541-740-4685
> Sent from an iPhone (so expect typos). 
>
> On Jul 19, 2011, at 10:34 PM, "Chris Fields" <cjfields at illinois.edu> 
> wrote:
>
> > This might be a disconnect between the HMMER3 version in bioperl-live 
> and the one in Kai's bioperl-hmmer3 repo.  I believe the one in 
> bioperl-live is newer.  Scott, can you give that a try?
> > 
> > chris
> > 
> > On Jul 19, 2011, at 9:45 PM, Thomas Sharpton wrote:
> > 
> >> Hi Scott,
> >> 
> >> Thanks for writing. I'm on the road at the moment so I have to be 
> briefer and less thorough than I'd like to be.
> >> 
> >> What you are observing is not the intended behavior. Oddly, it's not 
> what I recall obtaining in my tests on this software, though I was mostly 
> interested in hmmsearch at the time and may have been sloppier than I 
> should have been when it came to hmmscan.
> >> 
> >> What version of HMMER3 you're using? There have been some small 
> formatting changes in the past that might be causing a burp in the parser, 
> though I'm doubting it.
> >> 
> >> Kai Blin wrote some test scripts (found here: 
> bioperl-live/t/SearchIO/hmmer.t) that, if I recall correctly, evaluate 
> query/hit coordinates. It might be worth giving this a shot if you haven't 
> already.
> >> 
> >> Also, if you don't mind, I'm happy to run your code on your output file 
> on my end. It might help me diagnose the problem.
> >> 
> >> Sorry this is being a thorn in your side! I've cc'ed the list in case 
> anyone else has insight into this matter.
> >> 
> >> Best,
> >> Thomas
> >> 
> >> On Jul 19, 2011, at 10:43 AM, Givan, Scott A. wrote:
> >> 
> >>> Hi Thomas,
> >>> 
> >>> I'm using modules in the bipoerl-hmmer3 git repository to parse hmmscan
> >>> reports. When I parse the files and walk through the HSP's like:
> >>> 
> >>> while (my $hit = $rslt->next_model) {
> >>> 
> >>>    while (my $domain = $hit->next_hsp) {
> >>> 
> >>> And retrieve the "hit" coordinates like:
> >>> 
> >>>        print "hit coords: ", $domain->start('hit'), "-", 
> $domain->end('hit'),
> >>> "\n";
> >>> 
> >>> The coordinates returned correspond to what I would call the "query",
> >>> since they are for the sequence I fed to hmmscan to search the profile
> >>> database. Likewise, when retrieving the query coordinates like
> >>> $domain->start('query'), I get what I consider the "hit" coordinates,
> >>> since they are for the domain profile. Is this the intended behavior?
> >>> 
> >>> Thanks.
> >>> 
> >>> scott
> >>> 
> >>> -- 
> >>> Scott A. Givan
> >>> Associate Director
> >>> Informatics Research Core Facility
> >>> 240e Bond Life Sciences Center
> >>> Research Assistant Professor
> >>> Molecular Microbiology and Immunology
> >>> University of Missouri, Columbia
> >>> 
> >>> TEL 573-882-2948
> >>> FAX 573-884-9676
> >>> http://ircf.rnet.missouri.edu
> >>> 
> >>> 
> >>> 
> >> 
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
>
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