Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (303K) Freely available
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 (23)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Majoros, W. H.
Right arrow Articles by Salzberg, S. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Majoros, W. H.
Right arrow Articles by Salzberg, S. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 13 3601-3604
© 2003 Oxford University Press

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders

William H. Majoros*, Mihaela Pertea, Corina Antonescu and Steven L. Salzberg

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +1 301 838 0208; Fax: +1 301 610 5985; Email: bmajoros{at}tigr.org

We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis thaliana. Cases have been found where each of the genefinders outperforms each of the others, demonstrating the collective value of this ensemble of genefinders. These programs are all accessible through webservers at http://www.tigr.org/software.


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
 Genome ResHome page
V. Ter-Hovhannisyan, A. Lomsadze, Y. O. Chernoff, and M. Borodovsky
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
Genome Res., December 1, 2008; 18(12): 1979 - 1990.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
J. K. Hane, R. G.T. Lowe, P. S. Solomon, K.-C. Tan, C. L. Schoch, J. W. Spatafora, P. W. Crous, C. Kodira, B. W. Birren, J. E. Galagan, et al.
Dothideomycete Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum
PLANT CELL, November 1, 2007; 19(11): 3347 - 3368.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Saeys, P. Rouze, and Y. Van de Peer
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
Bioinformatics, February 15, 2007; 23(4): 414 - 420.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Hajarnavis, I. Korf, and R. Durbin
A probabilistic model of 3' end formation in Caenorhabditis elegans
Nucleic Acids Res., June 24, 2004; 32(11): 3392 - 3399.
[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.