[Bioperl-l] Fwd: hmmpfam

Jason Stajich jason at bioperl.org
Wed Jun 25 01:24:02 EDT 2008


forgot to cc list

From: Jason Stajich <jason at bioperl.org>
Date: Jun 25, 2008 2:23 PM
Subject: Re: [Bioperl-l] hmmpfam
To: Joonas Jämsen <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> 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
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason

-- 
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason



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