we would like to be able to have a data file containing a set of
sequences to use as a searchable database using FASTA or some other
search program in gcg.
how does one set up such a database in your own dir?
There are two ways:
1) Use a file of filenames. This is just a list of the sequence
files you want to search. Files in other directories must include
path information. (See your user guide for file format, but it's
pretty simple: header ended by ".." at end of line, one filename
per line.). Specify the library to search with "@file-of-filenames.fil".
2) You can make your own library file. This is preferred if your personal
database is of significant size (several hundred or more sequences). I
haven't done this in a long time, but the info should be in chapter 2 of
the GCG user guide.
Mike Lonetto lonetto at cgl.ucsf.edu
UCSF Dental School, Dept of Oral Biology, 513 Parnassus Avenue, HSW 604
San Francisco, CA 94143-0512