Skip Navigation


Bioinformatics Advance Access originally published online on May 14, 2004
Bioinformatics 2004 20(16):2878-2879; doi:10.1093/bioinformatics/bth315
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/16/2878    most recent
bth315v1
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 (36)
Right arrowRequest Permissions
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?

Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

Applications Note

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders

W. H. Majoros *, M. Pertea and S. L. Salzberg

Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA

Received on April 1, 2004; revised on April 28, 2004; accepted on May 3, 2004
Advance Access Publication May 14, 2004

Summary: We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes.

Availability: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate.

Contact: bmajoros{at}tigr.org

* To whom correspondence should be addressed.


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
 Proc. Natl. Acad. Sci. USAHome page
M. Novo, F. Bigey, E. Beyne, V. Galeote, F. Gavory, S. Mallet, B. Cambon, J.-L. Legras, P. Wincker, S. Casaregola, et al.
Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118
PNAS, September 22, 2009; 106(38): 16333 - 16338.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Enol. Vitic.Home page
M. Troggio, S. Vezzulli, M. Pindo, G. Malacarne, P. Fontana, F. M. Moreira, L. Costantini, M. S. Grando, R. Viola, and R. Velasco
ASEV Honorary Research Lecture 2007: Beyond the Genome, Opportunities for a Modern Viticulture: A Research Overview
Am. J. Enol. Vitic., June 1, 2008; 59(2): 117 - 127.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Q. Liu, A. J. Mackey, D. S. Roos, and F. C. N. Pereira
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Bioinformatics, March 1, 2008; 24(5): 597 - 605.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
N. Day, A. Hemmaplardh, R. E. Thurman, J. A. Stamatoyannopoulos, and W. S. Noble
Unsupervised segmentation of continuous genomic data
Bioinformatics, June 1, 2007; 23(11): 1424 - 1426.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K.-H. Ling, M.-A. Rajandream, P. Rivailler, A. Ivens, S.-J. Yap, A. M.B.N. Madeira, K. Mungall, K. Billington, W.-Y. Yee, A. T. Bankier, et al.
Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization
Genome Res., March 1, 2007; 17(3): 311 - 319.
[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
K. Knapp and Y.-P. P. Chen
An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
Nucleic Acids Res., January 12, 2007; 35(1): 317 - 324.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, and B. Morgenstern
AUGUSTUS: ab initio prediction of alternative transcripts.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W435 - W439.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. E. Allen and S. L. Salzberg
JIGSAW: integration of multiple sources of evidence for gene prediction
Bioinformatics, September 15, 2005; 21(18): 3596 - 3603.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. H. Majoros, M. Pertea, and S. L. Salzberg
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Bioinformatics, May 1, 2005; 21(9): 1782 - 1788.
[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.