Path: utzoo!utgpu!watserv1!watmath!uunet!cs.utexas.edu!read
From: read@cs.utexas.edu (Rob)
Newsgroups: bionet.molbio.genome-program
Subject: GenBank Parser
Keywords: genome,parser
Message-ID: <922@dimebox.cs.utexas.edu>
Date: 23 Sep 90 04:20:26 GMT
Organization: U. Texas CS Dept., Austin, Texas
Lines: 29



*  Does anyone have a lexer/parser for the GenBank Feature Table?

*  Would anone want one if wrote one?

I am seeking to avoid duplication of effort.  I work for the Biological
Workstation Group at the University of Texas Center for High
Performance Computing (UT-CHPC).  We are going to construct a logic
programming-based query interface to the feature table using the
experimental knowledge base LDL.  At present, LDL reads data
from a "flat" file in its own format.  Therefore, I need to translate
the GenBank distribution into that format.

I am a computer science student and new to the biological aspects
of this area.  From a computer science point of view, it seems
pretty obvious that the published feature table definition should
be easily parsed using widely available lexical anaylyzer and 
parser generator tools, like Flex/Lex and Bison/Yacc.

So I figure some one out there has already built a parser.
If not, I will do so.

Thanks for any response and looking for electronic contacts,
Rob

Robert L. Read				University of Texas
read@cs.utexas.edu			Center for High Performance
(512)-477-1240				Computation