Bioinformatics Advance Access published online on January 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk040
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1 Department of Biology, New York University, New York, NY 10003; Current address: Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854
* To whom correspondence should be addressed.
Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pair-wise distance comparisons algorithms, such as BLAST, COG, RBH, RSD, and INPARANOID, to determine gene orthology. By contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale due to the lack of efficiency and automation. Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes. Availability: http://nypg.bio.nyu.edu/orthologid/. Associate Editor: Keith A Crandall
Received July 10, 2005
Revised January 4, 2006
Accepted January 4, 2006
Article
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
Joanna C. Chiu 1 
,
Ernest K. Lee 2 * ,
Mary G. Egan 2,
Indra Neil Sarkar 3,
Gloria M. Coruzzi 4,
and
Rob DeSalle 2
2 Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024
3 Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024; Division of Library Services, American Museum of Natural History, New York, NY 10024
4 Department of Biology, New York University, New York, NY 10003
Ernest K. Lee, E-mail: elee{at}amnh.org
Abstract These authors contributed equally
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