From: ncbi-admin@ncbi.nlm.nih.gov on behalf of Wataru Fujibuchi
[wataru@ncbi.nlm.nih.gov]
Sent: Wednesday, May 30, 2001 3:01 PM
To: ncbi-seminar@ncbi.nlm.nih.gov
Subject: Seminar Reminder: Detection of protein 1D and 3D motifs

Room: B.38A, 8th floor conference room 
Date: 2:00 PM, Mon, 4 June 2001 
Local Multiple Alignment of Real Number Sequences: Detection of
1D and 3D Motifs

Dr Tatsuya Akutsu from Univ. Tokyo, currently visiting researcher at
Steven Brenner Lab., UC Berkeley, will be visiting NCBI in June.

He will be giving a talk on protein motifs. Everyone is welcome to
attend. He would like to talk with protein researchers and genetic
network researchers here.
If anyone is interested, please let me know.
-Wataru Fujibuchi

SPEAKER:
Tatsuya AKUTSU
Human Genome Center, Institute of Medical Science,
University of Tokyo
takutsu@ims.u-tokyo.ac.jp

ABSTRACT:
  We propose a new method to find motifs from multiple protein sequences and
multiple protein structures. The method consists of two parts: quantification
and local multiple alignment. In the former part, protein sequences and
protein structures are transformed into sequences of real numbers and real
vectors respectively. In the latter part, fixed length regions having similar
curves are located.
  A Gibbs sampling algorithm for sequences of real numbers/vectors is newly
developed for finding common regions. If the method is applied to protein
sequences, physico-chemical properties of amino acids can be taken into
account.
  We compared the method with a standard Gibbs sampling program using several
data. The results show that the method is very useful when the number of input
sequences is small and structural data is available.                           

This is a joint work with Dr. Katsuhisa HORIMOTO at
Saga Medical School.

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_/  Wataru Fujibuchi, Ph.D.,  Computational Biology Branch    _/
_/      National Center for Biotechnology Information         _/
_/   Bldg 45, Rm 6th Floor, NIH, 45 Center Drive, MSC 6510    _/
_/          Bethesda, MD 20892-6510 USA (301)435-5896         _/
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