Subsequence Searching

POSTMAST at gunbrf.bitnet POSTMAST at gunbrf.bitnet
Wed May 1 11:25:00 EST 1991


Dr. Snyder,
In a request posted to the genbank-bb of BIOSCI you said
> I am looking for some software that will allow me to extract subsequences
> from genbank or PIR.
> For example, I would like to be able to provide a keyword such as 'splice
> site' and have the program search genbank and return with a list of sequence
> names and the subsequence from each entry corresponding to my keyword.
If you have access to a VAX/VMS machine, I think you will find PIR's XQS
program SCAN function will do pecisely that.
The FASTA program, as modified and maintained by Dr. William R. Pearson
(wrp at biochsn.acc.virginia.edu) will extract similar as well as identical
sequences.  The PIR FILESERVer uses a FASTA program to search the current
PIR databases.  You can receive instructions on how to use the PIR FILESERVer
by send a mail message to FILESERV at GUNBRF.BITNET consisting of the following
commands
  HELP
  HELP SEARCH
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET



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