[EMBOSS] question!

[Jon Ison]

Dear FANG

The error message suggests that EMBOSS has not been configured to work with "genbank".
Every database you intend to use must be defined in one of the EMBOSS configuration
files "emboss.default" or ".embossrc".

"emboss.default" lives in the top-level emboss directory (e.g. /home/auser/emboss/emboss.default)
and is used for site-wide databases.

".embossrc" lives in your personal home directory and is used for your own databases (or for testing).

Please read the documentation which describes how to configure database access in these files:
http://emboss.sourceforge.net/docs/themes/Databases.html
http://emboss.sourceforge.net/admin/

Or ask your sysadmin to setup access for you (a better route if the database is a shared resource).

So far as I know, EMBOSS cannot read ensembl directly.

The answer to your last question is "It depends on which databases your installation is configured
to use" (see "emboss.default" and ".embossrc").

Good luck !

Cheers

Jon


> Dear EMBOSS people:
>
> I am a Ph.D. student in Clemson University in USA, who is using your
> EMBOSS software to extract 5' upstream of a list of genes. However, I met
> some problem when I use EMBOSS:
>
> 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?
>
> 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?
>
> 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.
>
> Thanks!
>
> I am looking forward to your reply.
>
> FANG WANG
> Department of Genetics and Biochemistry
> Clemson University
>
>
>
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