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Bioinformatics Advance Access originally published online on May 14, 2004
Bioinformatics 2004 20(16):2878-2879; doi:10.1093/bioinformatics/bth315
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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.


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