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
