Mihai Pop
is a Bioinformatics Scientist at
the Institute for Genomic
Research. He earned his PhD in
Computer Science from Johns
Hopkins University in 2000. His
research interests include
genome assembly and
comparative genomics.
Adam Phillippy
is a Bioinformatics Software
Engineer at The Institute for
Genomic Research. His
research interests include
comparative genomics, whole
genome alignment and
sequence assembly.
Arthur L. Delcher
is a Bioinformatics Scientist at
The Institute for Genomic
Research and Professor
Emeritus of Computer Science
at Loyola College in Maryland.
He earned his PhD in
Computer Science from Johns
Hopkins University in 1989 and
was a member of the
Informatics Research group at
Celera Genomics that
developed the human genome
assembly program.
Steven L. Salzberg, PhD
is the Senior Director of
Bioinformatics at TIGR and is a
Research Professor of
Computer Science and Biology
at Johns Hopkins University.
Keywords: assembly,
shotgun sequencing,
comparative genomics, open
source
Mihai Pop,
The Institute for Genomic
Research,
9712 Medical Center Drive,
Rockville, MD 20850, USA
Tel: +1 301 795 7000
Fax: +1 301 838 0208
E-mail: mpop@tigr.org
Comparative genome
assembly
Mihai Pop, Adam Phillippy, Arthur L. Delcher and Steven L. Salzberg
Date received (in revised form): 21st June 2004
Abstract
One of the most complex and computationally intensive tasks of genome sequence analysis is
genome assembly. Even today, few centres have the resources, in both software and hardware,
to assemble a genome from the thousands or millions of individual sequences generated in a
whole-genome shotgun sequencing project. With the rapid growth in the number of
sequenced genomes has come an increase in the number of organisms for which two or more
closely related species have been sequenced. This has created the possibility of building a
comparative genome assembly algorithm, which can assemble a newly sequenced genome by
mapping it onto a reference genome. We describe here a novel algorithm for comparative
genome assemb