Path: utzoo!attcan!uunet!husc6!bloom-beacon!mit-eddie!ll-xn!ames!umd5!uvaarpa!hudson!biochsn!wrp
From: wrp@biochsn.acc.virginia.edu (William R. Pearson)
Newsgroups: sci.bio
Subject: Re: What would you like to see in DNA sequencing tools
Message-ID: <434@hudson.acc.virginia.edu>
Date: 20 Jun 88 17:27:56 GMT
References: <5916@umn-cs.cs.umn.edu>
Sender: news@hudson.acc.virginia.edu
Reply-To: wrp@biochsn.acc.Virginia.EDU (William R. Pearson)
Organization: University of Virginia, Charlottesville
Lines: 38

In article <5916@umn-cs.cs.umn.edu> papowell@umn-cs.cs.umn.edu (Patrick Powell, Dept. CS. U-Minn) writes:
]I have been looking at the problem of building a general purpose
]set of tools for doing some of the computation associated with
]the DNA/RNA sequencing work.   One of the problems that I have is getting
]a wider perspective on the TYPES of tools that users want.
]
]1.  User interfaces:
]2.  Database Searching:
]3.	What types of searching do you want?
]4.  If you had a wish list,  what NEW facilties,  tools, commands, etc.,
]	would you want?
]
]Please mail me replies;  I will summarize in 2 weeks time.
]Prof. Patrick Powell, Dept. Computer Science, 136 Lind Hall, 207 Church St. SE,
]University of Minnesota,  Minneapolis, MN 55455 (612)625-3543/625-4002

	I believe that there are two deficiencies in current sequence
analysis software.

	(1) a powerful sequence editor/assembly program for building
DNA sequences from multiple sequence determinations.  Although the
computational tools are available for rapid sequence assembly, as are the
database tools for recording changes to a sequence assembly database and the
editing tools required to make corrections, these have not been put together
to built a high quality, rapid, easy to use sequence assembly program.

	(2) a general regular expression matching program for looking
at DNA or protein sequences.  Although regular expression matching
programs are common, a program appropriate for biological sequence analysis
should have the ability to specify a distance range over which matches
must take place.  For example, match the pattern ABC{6-10}NDEF would
match ABCNNNNNNDEF and ABCNNNNNNNNNNDEF but not ABCNNNNNDEF.  In addition,
such a program should recognize DNA or protein sequences, not be
confused by newlines, and provide answers that refer to residue
numbers, not line numbers.

	Bill Pearson
	wrp@virginia.EDU