[Bioperl-l] hmmer3.pm question re query and hit coordinates
Peng Zhou
zhoupenggeni at gmail.com
Wed Jul 11 17:45:00 UTC 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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