On 08/04/2011 11:27, Alessandro Bruselles wrote:
Hi all,
I'm not able to retrieve sequences starting from official gene symbols (e.g.
BCL2L10),
what db do I have to use?
You need a database you can search by gene name. If the database has
access through a website you can use the URL access method ... providing
a URL that returns with the sequence in a format that EMBOSS can read.
For UniProt:
DB uniprotgene [
type: "protein"
format: "swiss"
methodquery: "url"
url:
"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-gen:%s]+-ascii";
]
(the URL should be all in one line)
We will have other ways to do this in EMBOSS 6.4.0 when we enable gen
and other database search fields.
This is the output of whichdb:
*$ whichdb BCL2L10 -debug
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Warning: Cannot open division file '<null>' for database 'tsw'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'emblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trembl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'nbrf'
EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed*
You need to fix or comment out the tsw, emblnew, trembl and nbrf
databases to avoid those messages. whichdb tries all sequence databases
and is a good way to catch database that are not working (servers down,
data or index files not in the expected directory)
Hope this helps
Peter
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