Subject: new paper on sequence analysis

From: "Dimitris Agrafiotis" <[email-masked]>
Date: Fri, 18 Oct 1996 14:52:21 -0400

A new paper entitled "A New Method for Analyzing Protein Sequence
Relationships Based on Sammon Maps" is to appear in a forthcoming
issue of Protein Science. If you would like a pre-print, please
send me a note, including your postal address. A postscript version
of the paper is also available. The abstract follows below.

___________________________________________________________________

A New Method for Analyzing Protein Sequence Relationships Based on
Sammon Maps.

Dimitris K. Agrafiotis

3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Exton, PA
19341, USA. Tel: (610) 458-6045, Fax: (610) 458-8249, E-mail:
[email-masked]

ABSTRACT

Recent advances in gene sequencing and rational drug design have
re-emphasized the need for protein analysis, classification, and
structure and function prediction. In this paper, we introduce a
new method for analyzing protein sequences based on Sammon's non-
linear mapping algorithm. When applied to a family of homologous
sequences, the method is able to capture the essential features
of the similarity matrix, and provides a faithful representation
of chemical or evolutionary distance in a simple and intuitive
way. The merits of the new algorithm are demonstrated using
examples from the protein kinase family.
_________________________________________________________________

-- 
Dimitris K. Agrafiotis, PhD              | e-mail: [email-masked]
3-Dimensional Pharmaceuticals, Inc.      | tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | fax:    (610) 458-8249
Exton, PA 19341