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. [EMAIL PROTECTED] 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:[EMAIL PROTECTED] > Sent: Tuesday, June 10, 2008 1:50 PM > To: [EMAIL PROTECTED] > Cc: Peter Rice; Jay; [email protected] > 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 > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
