[EMBOSS] emboss.defaut to access the enspep
Peter Rice
pmr at ebi.ac.uk
Thu Aug 18 09:30:29 UTC 2005
Yoshida Yuichi wrote:
> Hi, everyone,
>
> There is the following descriptions in the document of showdb
> command (/usr/share/EMBOSS/doc/programs/text/showdb.txt)
>
>
>>% showdb
>>Displays information on the currently available databases
>>
>># Name Type ID Qry All Comment
>># ==== ==== == === === =======
>>enspep P OK OK OK ENSEMBL pep
>>enspepp P OK OK OK ENSEMBL pep predicted
>
>
> But I can't access the enspep (ENSEMBL pep) and enspepp
> (ENSEMBL pep predicted) by the showdb command.
>
> How should I describe the emboss.default (or .embossrc) to
> be able to access the enspep and enspepp.
The current showdb.txt file does not use enspep or enspepp as databases. A
little history ...
We generate the showdb.txt file from EMBOSS documentation on the website
http://emboss.sourceforge.net/apps/showdb.html for each release. The usage
example and the example output are in turn generated from our QA test suite.
Your installation's showdb.txt file may be from an old release of EMBOSS,
before we started to build the files from sourceforge.
The older versions of showdb.txt used the databases installed at HGMP/RFCGR,
where the EMBOSS developers were working. This institute has now closed and
the development has moved to all be at EBI. The showdb.txt file was updated a
year ago in release 2.10.0 when we started to move files from the HGMP website
to sourceforge.
If I recall correctly, HGMP's enspep and enspepp databases pointed to their
SRS server, which has also closed.
The ENSPEP database can be defined (for single entries only) using the Sanger
Centre's SRS server:
DB enspep [ type: "N" method: "SRSWWW"
format: "fasta"
url: "http://srs.sanger.ac.uk/srs7bin/cgi-bin/wgetz"
dbalias: "ensemblpep"
comment: "ensembl pep"
]
To define is for multiple entries, use "methodquery" instead of "method" -
this will allow you to use wildcard IDs.
There is a list of publicly available SRS servers at
http://downloads.lionbio.co.uk/publicsrs.html (liked to the EBI server's fron
page. I can find nothing to match HGMP's "enspepp" database - unless it was
simply a duplicate of the enspep database with a different access method.
Sadly, the HGMP SRS server had more databases than any other server in the
world. Some of them were not available anywhere else.
HGMP may have also indexed enspep and enspepp in some other way (with dbifasta
or dbiflat), using the ENSEMBL flatfiles from ftp.ensembl.org for example
ftp://ftp.ensembl.org/pub/current_human/data/fasta/pep/ (for FASTA format
files) or ftp://ftp.ensembl.org/pub/current_human/data/embl/pep/ for "embl"
format files. There are separate files for some species that HGMP may have
used for their two databases enspep and enspepp.
We are working on ways to generate more information from showdb so that we can
find out more about the database definitions (for sites that still exist!) in
a future release.
Hope that helps
Peter Rice
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