[EMBOSS] sequence retrieval

[david.bauer at bayerhealthcare.com]

Hi,

the database section of the adminguide
http://emboss.sourceforge.net/docs/adminguide/node37.html
describes all the emboss database indexing methods.
There is also a specific chapter on fasta files
http://emboss.sourceforge.net/docs/adminguide/node56.html
which describes the different forms of fasta files. It is important to 
specify the correct type corresponding to the structure of the sequence 
header line.
And also use full path names for the "Database directory" because relative 
path names like "." can cause problems on some systems.

If you still get trouble, send me the section you have in .embossrc, so I 
can have a look at it.
Hope this helps,

Cheers,
David.


emboss-bounces at lists.open-bio.org schrieb am 10/06/2008 22:15:35:

> Daniel:
> I tried seqret in different ways.
> My problem is EMBOSS is not recognizing my master sequence file (which 
is in
> fasta form) as my private database. Even after I did the indexing using
> dbifasta.
> When seqret is asking me to input sequence(s), I am not able to figure 
out
> what exactly it accepts.
> I tried dbname:ID, dbname:@listfile.
> I also tried a crude way of copy pasting my master file and listfile in
> "embl" folder in EMBOSSwin folder and try the same syntax (embl:ID,
> embl:@listfile etc.
> These did not work.
> I am assuming that my master file is not being recognized as a private 
DB.
> I wanted to define my database in .embossrc file. I could not figure 
this
> out either.
> Jay
> 
> -----Original Message-----
> From: Daniel Barker [mailto:db60 at st-andrews.ac.uk] 
> Sent: Tuesday, June 10, 2008 1:50 PM
> To: rls at ebi.ac.uk
> Cc: Peter Rice; Jay; emboss at lists.open-bio.org
> Subject: Re: [EMBOSS] sequence retrieval
> 
> Dear Jay,
> 
> Are you simply trying to extract specific sequences from a Fasta-format
> file? The EMBOSS program to do it is seqret, or maybe seqretsplit:
> 
> http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqret.html
> 
> 
http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqretsplit.html
> 
> As Peter Rice suggests, you can do stuff to speed the access up, but
> it'll work without that.
> 
> Best regards,
> 
> Daniel
> 
> -- 
> Daniel Barker
> http://bio.st-andrews.ac.uk/staff/db60.htm
> The University of St Andrews is a charity registered in Scotland :
> No SC013532
> 
> 
> ------------------------------------------------------------------
> University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> 
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