[EMBOSS] embossrc - configure database NPRD and AEdb

[Peter Rice]

Dear Giovanni
>>Hi all,
>>I'm trying to configure this two databases in my .embossrc -
>>emboss_default
>>, but I didn't managed to get it works:
>>
>>http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+3Xn_71Qks76+-lib+NUCLEOSOME
>>http://www.ebi.ac.uk/asd-srv/AEdb-query.cgi?method=MAIN&visit=first

For the SRS database, yes you should use SRSWWW ... but ...

The NUCLEOSOME database at that site has problems:

No standard field names (not even ID)
Parser errors in SRS
No text view
Non-standard format
No FASTA format view

Even if we try the URL method, there seems to be no URL to produce output that 
EMBOSS can understand. From the list of public SRS servers, this is the only 
server that has this database.

The only solution at present is to write a script (in Perl, for example) that 
can fetch and reformat an entry from this server, and write it in (for 
example) FASTA format, and to use this script with the "external" access 
method from EMBOSS.

For the EBI Alternate Exons Database query:

Again, there is no URL that returns a standard format EMBOSS can use, so a 
script is the best solution. You also need to decide what sequence you need (I 
assume the exon, but there are other sequences in the results)

We are working on ways to use more complex queries and more data formats - as 
part of the EMBRACE project at EBI. But this will take time before it can be 
used for these queries.

Hope this helps,

Peter