Skip Navigation



Bioinformatics Advance Access published online on February 26, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth153
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/12/1850    most recent
bth153v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by McAuliffe, J. D.
Right arrow Articles by Jordan, M. I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by McAuliffe, J. D.
Right arrow Articles by Jordan, M. I.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received September 20, 2003
Revised January 4, 2004
Accepted January 20, 2004

Article

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny

Jon D. McAuliffe 1, Lior Pachter 2, Michael I. Jordan 3*

1 1Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA 94720, USA
2 2Department of Mathematics, University of California, 970 Evans Hall, Berkeley, CA 94720, USA
3 1Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA 94720, USA; 3Division of Computer Science, University of California, 387 Soda Hall, Berkeley, CA 94720, USA

* To whom correspondence should be addressed. E-mail: jordan{at}cs.berkeley.edu.


  Abstract

Motivation: Phylogenetic shadowing is a comparative genomics principle which allows for the discovery of conserved regions in sequences from multiple closely-related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints.

Results: We show how GHMPs can be used to predict complete shared gene structures in multiple primate sequences. We also describe SHADOWER, our implementation of such a prediction system. We find that SHADOWER outperforms previously reported ab initio gene finders, including comparative human-mouse approaches, on a small sample of diverse exonic regions. Finally, we report on an empirical analysis of SHADOWER's performance which reveals that as few as five well-chosen species may suffice to attain maximal sensitivity and specificity in exon demarcation.

Availability: A Web server is available at http://bonaire.lbl.gov/shadower.


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
W. H. Majoros and U. Ohler
Complexity reduction in context-dependent DNA substitution models
Bioinformatics, January 15, 2009; 25(2): 175 - 182.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. DeCaprio, J. P. Vinson, M. D. Pearson, P. Montgomery, M. Doherty, and J. E. Galagan
Conrad: Gene prediction using conditional random fields
Genome Res., September 1, 2007; 17(9): 1389 - 1398.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. Bofkin and N. Goldman
Variation in Evolutionary Processes at Different Codon Positions
Mol. Biol. Evol., February 1, 2007; 24(2): 513 - 521.
[Abstract] [Full Text] [PDF]

Home page
 BiostatisticsHome page
N. Beerenwinkel and M. Drton
A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data
Biostat., January 1, 2007; 8(1): 53 - 71.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
C. N. Dewey and L. Pachter
Evolution at the nucleotide level: the problem of multiple whole-genome alignment.
Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R51 - R56.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. C. King, J. Taylor, L. Elnitski, F. Chiaromonte, W. Miller, and R. C. Hardison
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
Genome Res., August 1, 2005; 15(8): 1051 - 1060.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. D. McAuliffe, M. I. Jordan, and L. Pachter
Subtree power analysis and species selection for comparative genomics
PNAS, May 31, 2005; 102(22): 7900 - 7905.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
R. H. Brown, S. S. Gross, and M. R. Brent
Begin at the beginning: Predicting genes with 5' UTRs
Genome Res., May 1, 2005; 15(5): 742 - 747.
[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.