Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 (40)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Zmasek, C. M.
Right arrow Articles by Eddy, S. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zmasek, C. M.
Right arrow Articles by Eddy, S. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 17 no. 9 2001
Pages 821-828
© 2001 Oxford University Press

A simple algorithm to infer gene duplication and speciation events on a gene tree

Christian M. Zmasek and Sean R. Eddy

Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA

Received on January 24, 2001 ; revised on April 5, 2001 ; accepted on April 6, 2001

Motivation: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein’s function than paralogous sequences (that diverged by gene duplication), because duplication enables functional diversification. The utility of phylogenetic information in high-throughput genome annotation (‘phylogenomics’) is widely recognized, but existing approaches are either manual or indirect (e.g. not based on phylogenetic trees). Our goal is to automate phylogenomics using explicit phylogenetic inference. A necessary component is an algorithm to infer speciation and duplication events in a given gene tree.

Results: We give an algorithm to infer speciation and duplication events on a gene tree by comparison to a trusted species tree. This algorithm has a worst-case running time of O() which is inferior to two previous algorithms that are O() for a gene tree of sequences. However, our algorithm is extremely simple, and its asymptotic worst case behavior is only realized on pathological data sets. We show empirically, using 1750 gene trees constructed from the Pfam protein family database, that it appears to be a practical (and often superior) algorithm for analyzing real gene trees.

Availability: http://www.genetics.wustl.edu/eddy/forester

Contact: zmasek{at}genetics.wustl.edu; eddy{at}genetics.wustl.edu


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
 Mol Biol EvolHome page
S. Castellano, A. M. Andres, E. Bosch, M. Bayes, R. Guigo, and A. G. Clark
Low Exchangeability of Selenocysteine, the 21st Amino Acid, in Vertebrate Proteins
Mol. Biol. Evol., September 1, 2009; 26(9): 2031 - 2040.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B. A. Kristoffersen, A. Nerland, F. Nilsen, J. Kolarevic, and R. N. Finn
Genomic and Proteomic Analyses Reveal Non-Neofunctionalized Vitellogenins in a Basal Clupeocephalan, the Atlantic Herring, and Point to the Origin of Maturational Yolk Proteolysis in Marine Teleosts
Mol. Biol. Evol., May 1, 2009; 26(5): 1029 - 1044.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Cheng, S. Hartmann, M. Gupta, J. G. Ibrahim, and T. J. Vision
A hierarchical model for incomplete alignments in phylogenetic inference
Bioinformatics, March 1, 2009; 25(5): 592 - 598.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. J. Sanderson, D. Boss, D. Chen, K. A. Cranston, and A. Wehe
The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
Syst Biol, June 1, 2008; 57(3): 335 - 346.
[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
 GeneticsHome page
M. W. Hahn, J. P. Demuth, and S.-G. Han
Accelerated Rate of Gene Gain and Loss in Primates
Genetics, November 1, 2007; 177(3): 1941 - 1949.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev
Automatic genome-wide reconstruction of phylogenetic gene trees
Bioinformatics, July 1, 2007; 23(13): i549 - i558.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Jothi, E. Zotenko, A. Tasneem, and T. M. Przytycka
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
Bioinformatics, April 1, 2006; 22(7): 779 - 788.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Ternes, P. Sperling, S. Albrecht, S. Franke, J. M. Cregg, D. Warnecke, and E. Heinz
Identification of Fungal Sphingolipid C9-methyltransferases by Phylogenetic Profiling
J. Biol. Chem., March 3, 2006; 281(9): 5582 - 5592.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Li, A. Coghlan, J. Ruan, L. J. Coin, J.-K. Heriche, L. Osmotherly, R. Li, T. Liu, Z. Zhang, L. Bolund, et al.
TreeFam: a curated database of phylogenetic trees of animal gene families
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D572 - D580.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J.-F. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann, and G. Perriere
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Bioinformatics, June 1, 2005; 21(11): 2596 - 2603.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Lazareva-Ulitsky, K. Diemer, and P. D. Thomas
On the quality of tree-based protein classification
Bioinformatics, May 1, 2005; 21(9): 1876 - 1890.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. Subramanian and S. Kumar
Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes
Genome Res., May 1, 2003; 13(5): 838 - 844.
[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.