[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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