[Bioperl-l] (no subject)

Dhr. R. de Jonge ronnie.dejonge at gmail.com
Tue Jul 22 10:36:17 EDT 2008


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
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

2008/7/21, Chris Fields <cjfields at uiuc.edu>:
> Ya beat me to it!  I agree, this is the best way to go, and it would
> save an extra BLAST run (though if you need it Diego's bl2seq
> suggestion is the way to go).
>
> chris
>
> On Jul 21, 2008, at 11:31 AM, Dave Messina wrote:
>
>> You know which protein sequence corresponds to which cDNA sequence,
>> so I
>> think you could also:
>>
>> - take the start and end coordinates of the domain in the protein
>> (from the
>> HMMer output)
>> - convert those into the start and end coordinates of the domain in
>> the cDNA
>> - use the subseq() method to extract the subsequence of the cDNA
>>
>>
>> Dave
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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