(Follow-up to bionet.biology.computational)
Techniques for the optimal Multiple Alignment of Protein (and Nucleotide)
Sequences were the focus of the Guest Lecture given by Dr. John Kececioglu
of the Department of Computer Science at the University of Georgia, Athens,
USA, on July 13 1995, at the electronic conferencing system BioMOO.
The transcript is available at the following location (WWW/hypertext):
http://www.techfak.uni-bielefeld.de/bcd/Lectures/kececioglu.html
In the form of a Questions and Answers session, the Carrillo-Lipman
approach to Multiple Alignment was discussed, with a special emphasis
on practical considerations. The corresponding software, known as
MSA 1.0, has recently been improved yielding MSA 2.1, currently the most
powerful tool for optimal multiple sequence alignment. Dr. Kececioglu, who
co-authored the corresponding publications and code [LAK89] [GKS95],
explained the new ideas behind MSA 2.1. The meeting closed with some
remarks about alternative lower bounds, and a way of calculating near-
optimal alignments using a local search technique.
Dr. Kececioglu was special guest in Robert Giegerich's study group, which
was one of 7 groups of students that participated in the Summer 1995
Biocomputing Course organized by the VSNS Biocomputing Division /
Bielefeld University, sponsored by GNA's Virtual School of Natural Sciences,
and the Association for the Promotion of Science and Humanities in Germany.
(see http://www.techfak.uni-bielefeld.de/bcd/welcome.html)
The lecture was held in the virtual classroom at BioMOO [And94], and
both John Kececioglu and Robert Giegerich connected from the 1994 Dagstuhl
meeting on Molecular Bioinformatics. Other participants connected from John
Hopkins School of Medicine / USA, Harvard Medical School / USA, and
Bielefeld / Germany.
References:
[And94] Christopher Anderson, Cyberspace Offers Chance To Do 'Virtually'
Real Science. Science 1994;264:900-901
BioMOO URL: http://bioinfo.weizmann.ac.il:8888/
[GKS95] S. K. Gupta, J. Kececioglu, A. A. Schaeffer, Improving the
Practical Space and Time Efficiency of the Shortest-Paths
Approach to Sum-of-Pairs Multiple Sequence Alignment.
J Computational Biology, to appear.
URL: http://ibc.wustl.edu/msa.html
[LAK89] D. J. Lipman, S. F. Altschul, J. Kececioglu, A Tool for
Multiple Sequence Alignment. Proc Nat Acad Sci USA 1989;86:4412-4415
--
best wishes,
georg
fuellen at dali.Mathematik.Uni-Bielefeld.DE, fuellen at MIT.EDUhttp://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html
