[EMBOSS] external and app
Guy Bottu
gbottu at ben.vub.ac.be
Fri Jun 3 10:03:18 UTC 2005
On Fri, Jun 03, 2005 at 11:15:10AM +0200, Alexis Torrano Martinez wrote:
> I am trying to execute hmmsearch from EMBOSS. This way I want to have
> a kind of wrap over the DDBB and retrieval apps.
>
>
> DB Pfam [
> method: "app"
> comment: "Pfam with HMMER indexing"
> app: "$HMMERBIN/hmmsearch $EMBOSS_DATA/pfam/Pfam_ls %s"
> ]
Dear Alexis,
Your problem is as good as certain that the program defined as "app"
should return a sequence to standard output, so that EMBOSS can take it.
And this is not what hmmsearch does. Furthermore, hmmsearch searches a HMM
against a databank of sequences ; you seem to want to search a sequence
against a databank of HMM's (Pfam_ls), for which you need hmmpfam. It is
maybe a good idea to install the Embassadir HMMER. Note however that
ehmmpfam needs the user to specify where the databank is. At the BEN site
I have a little bit "hacked" the program so that it uses Pfam_ls by
default (and still lets the user choose an alternative). If you are
interested I can send you a mail with "how to".
Guy Bottu,
Belgian EMBnet Node
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