GlimmerM, Exonomy and Unveil: Three ab initio eukaryotic genefinders

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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3601-3604
Number of pages4
JournalNucleic Acids Research
Volume31
Issue number13
DOIs
StatePublished - Jul 1 2003
Externally publishedYes

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Decision Trees
Eukaryota
Arabidopsis
Software
Genes

ASJC Scopus subject areas

  • Genetics

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GlimmerM, Exonomy and Unveil : Three ab initio eukaryotic genefinders. / Majoros, William H.; Pertea, Mihaela; Antonescu, Corina; Salzberg, Steven L.

In: Nucleic Acids Research, Vol. 31, No. 13, 01.07.2003, p. 3601-3604.

Research output: Contribution to journalArticle

Majoros, William H. ; Pertea, Mihaela ; Antonescu, Corina ; Salzberg, Steven L. / GlimmerM, Exonomy and Unveil : Three ab initio eukaryotic genefinders. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 13. pp. 3601-3604.
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