Skip Navigation


Bioinformatics Advance Access originally published online on January 12, 2006
Bioinformatics 2006 22(6):699-707; doi:10.1093/bioinformatics/btk040
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/6/699    most recent
btk040v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (13)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Chiu, J. C.
Right arrow Articles by DeSalle, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chiu, J. C.
Right arrow Articles by DeSalle, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OrthologID: automation of genome-scale ortholog identification within a parsimony framework

Joanna C. Chiu 1,{dagger}, Ernest K. Lee 2, Mary G. Egan 2, Indra Neil Sarkar 2,3, Gloria M. Coruzzi 1,* and Rob DeSalle 2

1Department of Biology, New York University New York, NY 10003, USA
2Division of Invertebrate Zoology, American Museum of Natural History New York, NY 10024, USA
3Division of Library Services, American Museum of Natural History New York, NY 10024, USA

*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 pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing 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/

Contact: gloria.coruzzi{at}nyu.edu

Received on July 10, 2005; revised on January 4, 2006; accepted on January 4, 2006

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
O. Sakarya, K. S. Kosik, and T. H. Oakley
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
Bioinformatics, March 1, 2008; 24(5): 606 - 612.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
T. Frickey, V. A. Benedito, M. Udvardi, and G. Weiller
AffyTrees: Facilitating Comparative Analysis of Affymetrix Plant Microarray Chips
Plant Physiology, February 1, 2008; 146(2): 377 - 386.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Perin
GreenPhylDB: a database for plant comparative genomics
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D991 - D998.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. S. Walker, N. Stiffler, and A. Barkan
POGs/PlantRBP: a resource for comparative genomics in plants
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D852 - D856.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
E. A. Kellogg
Progress and challenges in studies of the evolution of development
J. Exp. Bot., October 1, 2006; 57(13): 3505 - 3516.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.