[Bioperl-l] (no subject)

Dhr. R. de Jonge ronnie.dejonge at gmail.com
Tue Jul 22 11:27:48 EDT 2008

Thanks, I'm trying the options right now!

update: Seems I get it roling now using the bl2seq directly in my hmm
parser script!
The results look very promising, and no false positives (by quick
visual inspection!).


2008/7/22, Chris Fields <cjfields at uiuc.edu>:
> On Jul 22, 2008, at 9:36 AM, Dhr. R. de Jonge wrote:
>> Hi all,
>> Thanks for the very quick responses. I've been trying to fix it today,
>> trying both the bl2seq method and the direct approach. Unfortunately,
>> I'm unable to fix either of the two.
>> At the moment I'm trying to get the direct approach working, however,
>> I'm not able to obtain the hit_start and hit_end numbers of the
>> domain. It seems that these methods, which are not implemented in the
>> Bio::Search::HSP::HMMERHSP module (which I used to obtain the domain
> I believe the query is your sequence and the 'hits' are the HMMs (been
> a while since I used HMMER though).  In this case you don't want the
> hit start/end, you want $hsp->start('query')/$hsp->end('query') (or
> $hsp->query->start/$hsp->query->end, which should be the same thing).
>> sequence). I've screened through the appropriate modules, with no
>> luck. Is there a method to obtain these hit_start/hit_end figures by
>> parsing? Or is there a better method?
>> Many thanks again!
>> Cheers
>> Ronnie
> See the HOWTO for SearchIO for more methods.
> http://www.bioperl.org/wiki/HOWTO:SearchIO
> Some hit/HSP methods for HMMER aren't implemented, IIRC.  For an
> alternative faster approach you can try Sendu's hmmer_pull
> implementation.
> chris

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