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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2878-2879
Number of pages2
JournalBioinformatics
Volume20
Issue number16
DOIs
StatePublished - Nov 1 2004
Externally publishedYes

Fingerprint

Open Source
Markov Model
Genes
Gene
Tree Decomposition
Aspergillus fumigatus
Toxoplasma
C++
Annotation
Genome
Aspergillus
Hidden Markov models
Prediction
Decomposition
Architecture

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

TigrScan and GlimmerHMM : Two open source ab initio eukaryotic gene-finders. / Majoros, W. H.; Pertea, Mihaela; Salzberg, Steven L.

In: Bioinformatics, Vol. 20, No. 16, 01.11.2004, p. 2878-2879.

Research output: Contribution to journalArticle

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