[EMBOSS] emboss.defaut to access the enspep

[Peter Rice]

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