By Robert C. Edgar
ESI Special Topics,
January 2006
Citing URL - http://www.esi-topics.com/nhp/2006/january-06-RobertCEdgar.html
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Robert C. Edgar answers a few questions about this month's
new hot paper in the field of Computer Science.
From
•>>January 2006
Field:
Computer Science
Article Title: MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Authors: Edgar, RC
Journal: BMC BIOINFORMATICS
Volume:
5: art. no.-113
Page:
Year: AUG 19 2004
* Univ Calif Berkeley, Dept Plant & Microbial Biol, 461 Koshland Hall, Berkeley, CA 94720 USA.
* Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA.
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 Does
it describe a new discovery or a new methodology that's useful to
others? Why do you think your paper is highly cited?
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“...MUSCLE offers an attractive combination of features: high biological accuracy, the ability to handle large datasets and fast execution times.”
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It describes a new computer program in a software category that
is widely used among biologists, second only to sequence database
search programs such as BLAST—the Basic Local Alignment Search
Tool for comparing gene and protein sequences—in terms of
widespread use and importance in research. While several other
programs in this category, known as multiple sequence alignment, are
already available, MUSCLE offers an attractive combination of
features: high biological accuracy, the ability to handle large
datasets and fast execution times. An improved program in this area
may be rapidly adopted by a large number of researchers.
Could
you summarize the significance of your paper in layman's terms?
Multiple sequence alignment is a method for comparing genes—expressed
as DNA or protein sequences—that are related by virtue of having a
common evolutionary ancestor. This analysis can offer valuable clues
regarding the functions of genes which have not yet been
experimentally characterized, suggesting directions for research in
fundamental biology and medicine.
How
did you become involved in this research?
I'm a retired businessman with no academic title or affiliation
in the usual sense. I do research as a vocation. I have a Ph.D. in
theoretical physics—from many years ago. After building and
selling a software company, I was exploring possible directions for
the next phase of my career when I met Kimmen Sjölander of the
Bioengineering faculty at UC Berkeley. Kimmen had an interest in
multiple sequence alignment algorithms but lacked the resources to
implement some of her ideas. I was excited by the opportunity to
work in computational biology, so I offered my skills as a software
engineer and we began a collaboration which lead to several
publications. Subsequently I started my own work which led to the
development of the MUSCLE algorithm.
Robert C. Edgar, Ph.D.
Mill Valley, CA, USA
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ESI Special Topics,
January 2006
Citing URL - http://www.esi-topics.com/nhp/2006/january-06-RobertCEdgar.html
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