[EMBOSS] Configuring EMBOSS to use getz

Peter Rice pmr at ebi.ac.uk
Wed Oct 8 15:55:48 UTC 2003

yann-francois.bizouerne at bayercropscience.com wrote:
> I am trying to use the method "srs".
> I am using Emboss  2.7.1 and SRS 7.1.
> In my emboss.default file, I have :
>    DB Nrl3dGetz [
>    methodquery: srs
>    format: pir
>    type: P
>    comment: "NRL 3D using SRS"
>    app: getz
>    dbalias:NRL3D
>    methodall: direct
>    file: "*.seq"
>    dir: $emboss_data_dir/nrl_3d
>    ]

Quick reply (it's a very busy day :_)

 From memory, SRS has a problem with PIR formatted databases. It does 
not report the entry in a format that EMBOSS recognizes (try getz -e to 
see what the entry looks like).

You may find the SRSFASTA methodquery works better (use format fasta).

Hope this helps - if not, ask me again!!!

Peter Rice

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