[Bioperl-l] hmmpfam

[Jason Stajich]

yeah  - you get it as a string, you make a sequence object, you write  
it out as fasta. I'm sure someone on the list can help if you can't  
figure out how to do this.
Read the sequence howto, you want to use Bio::Seq to make the  
sequence and Bio::SeqIO to write the sequence.

  I don't know if you want the whole sequence or just what was  
matched by the profile search.
Please continue to reply to questions to the mailing list.

-jason
On Jun 26, 2008, at 5:16 AM, Joonas Jämsen wrote:

> Thanks,
>
> Is there no way to get the sequence out in fasta format? I have  
> like 25000 sequences to extract. I have no clue as to how to do  
> this at the moment.
>
> Best regards,
> Joonas.
>
> Jason Stajich wrote:
>> forgot to cc list From: *Jason Stajich* <jason at bioperl.org  
>> <mailto:jason at bioperl.org>>
>> Date: Jun 25, 2008 2:23 PM
>> Subject: Re: [Bioperl-l] hmmpfam
>> To: Joonas Jämsen <jajams at utu.fi <mailto:jajams at utu.fi>>
>> you can get the sequence as a string, but it will have the gaps  
>> and other symbols inserted.
>>  See the SEARCHIO Howto for getting query and hit sequence as a  
>> string or a multiple-alignment of the query and hit pair  
>> (get_aln). -jason
>>  On 6/24/08, *Joonas Jämsen* <jajams at utu.fi  
>> <mailto:jajams at utu.fi>> wrote:
>>     Hello,
>>     Is it possible to just get the FASTA sequence of a specified  
>> domain
>>     (by name) above a certain threshold found with hmmpfam? I  
>> could not
>>     find this functionality in the packages I was referred to  
>> recently.
>>     Joonas Jämsen.
>>     _______________________________________________
>>     Bioperl-l mailing list
>>     Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open- 
>> bio.org>
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>> -- 
>> Jason Stajich
>> jason at bioperl.org <mailto:jason at bioperl.org>
>> http://bioperl.org/wiki/User:Jason
>> -- 
>> Jason Stajich
>> jason at bioperl.org <mailto:jason at bioperl.org>
>> http://bioperl.org/wiki/User:Jason<jajams.vcf>