The Fourth DIMACS International
Algorithm Implementation Challenge:
Two Problems in Computational Biology:
Fragment Assembly and Genome Rearrangements
In conjunction with its Special Year on Mathematical Support for
Molecular Biology, the Center for Discrete Mathematics and Theoretical
Computer Science (DIMACS) invites participation in an international
Implementation Challenge focussed on two problems from Computational
Molecular Biology: Sequence Assembly (the problem of reconstructing a DNA
sequence knowing only the sequences of many possibly overlapping fragments) and
Genome Rearrangements (the problem of comparing two orders of genes).
The Implementation Challenge will take place between September 1994 and
August 1995. Participants are invited to carry out research projects
related to these problem areas and to present research papers at a
DIMACS workshop to be held in September 1995. A refereed workshop
proceedings will be published.
Challenge materials are also available via anonymous ftp from
This directory also contains some
general information .
Lastest news are found in
There still is a large gap in Computational Molecular Biology between
biological application and algorithmic work aimed at answering
biological questions. It is the goal of this implementation challenge
to help bridge this gap.
is the problem of reconstructing a DNA sequence knowing only the
sequences of many overlapping fragments of it.
is the problem of comparing two orders of
genes under the assumption that one order is transformed into another
by a series of rearrangments. For both problems there exist algorithms
and software that in the case of fragment assembly is widely used.
- Ellson Chen, Applied Biosystems
- Sorin Istrail, Sandia National Laboratory
- David Johnson, AT&T Bell Laboratories
- John Kececioglu, UC Davis
- Joachim Messing, Rutgers University
- Joseph Nadeau, Jackson Laboratory
- Pavel Pevzner, Pennsylvania State University
- Peter Rice, Sanger Center
- Martin Vingron, German National Research Center for Computer Science
- Michael Waterman, University of Southern California
Next: Call for Participation
Contacting the Center
Document last modified on November 2, 1998.