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

Wibowo Arindrarto w.arindrarto at gmail.com
Wed Jul 11 17:25:44 EDT 2012

Hi everyone,

Just as an additional info that might be useful:

The current Biopython parser for the plain text format parses the very
first line to find out which HMMER flavor produces the result. Both 'hmm
from' and 'hmmto' are query coordinates if the flavor is hmmsearch
or phmmer; and they're hit coordinates if the flavor is hmmscan.

This information is not available in other HMMER command line output
formats (tblout and domtblout), which as Peter has mentioned, required
us to treat different flavors of the table output as different formats
for the time being.
Fortunately, after contacting the HMMER developers they mentioned that this
is not the case anymore in their development branch (and their future
planned release).

Hope that helps :),

On Wed, Jul 11, 2012 at 11:00 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Jul 11, 2012 at 8:02 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> Peng,
>> Has this been filed as a bug yet?
>>     https://redmine.open-bio.org/projects/bioperl
>> Seems like it would be fairly easy to fix, but I want to track it just in case.
>> chris
> Hi all,
> This could be the unfortunate fact that hmmscan and
> hmmsearch return very similar tabular output, but
> with query and hit interchanged. i.e. You need some
> extra information to know which way round they are
> (not possible with the current output). This was an
> issue in Bow's Biopython SearchIO project - which
> for the moment he solved by handling this as two
> hmmer file formats. In the medium term we're hoping
> hmmer3 will add some header information or something.
> Peter

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