[EMBOSS] question!

[Peter Rice]

Dear Fang,

> I installed EMBOSS 2.10.0 in on windowsXP PC.  However, when I use command 
> "extractfeat genbank:*", it does not work. The error message is "Error:uable 
> to read sequence 'genbank:4101655', Died: extractfeat termined:Bad value for 
> '-sequence' and no prompt".  But it work fine with "extractfeat 
> embl:AK222810".Do you know the reason?

If you used the database definitions provided with EMBOSS ... your genbank is 
possibly
pointing to the CBR  server in Canada which has now closed.

There is also a problem with the way SRS servers define the GI number - there 
are now servers that index it, but as "gid" not as "gi" which EMBOSS 
anticipated. We sill change the field name in the next release of EMBOSS.


To test whether yuor genbank definition works, you could try the ID
We are now at release 4.0.0 which allows "gi" as a search field. Earlier 
versions only had "sv" (sequence version) ... whether that is indexed depends on 
the database provider. Indexing GenBank in EMBOSS does allow GI searches.

> Is there any way to access ENsembl database. Is there any new version of 
> EMBOSS which could support more databases which could installed in windowsXP?

Ah, you are running EMBOSS under windows? embosswin was provided by Andre 
Blavier up to EMBOSS 2.10.0. We now provide a beta release of EMBOSS 4.0.0 for 
windows (nobody did version 3.0.0 for windows).

Hmmmm ... we need to make that more obvious on the EMBOSS website. EMBOSSWIN is 
available by FTP from emboss.open-bio.org/pub/EMBOSS/windows/ ... only a few 
brave people have tested it so far, but they report that it is working.

> Are all the databases which EMBOSS connected are the latest version? since I 
> found some database do not give the same results as what I get from the 
> database directly.

That depends on where the databases are. There is a list of SRS servers you can 
check for the number of entries and the date they were indexed:

http://downloads.biowisdomsrs.com/publicsrs.html

for example:

DB genbank [ type: N method: srswww format: genbank
    url: "http://iubio.bio.indiana.edu/srsbin/cgi-bin/wgetz"
    dbalias: "genbankrelease"
    fields: "gi sv des org key"
    comment: "Genbank IDs" ]

You can also try Entrez databases in EMBOSS 4.0.0 ... I wonder how many users 
have been using entrez as an access method?

Hope that helps

Peter Rice