GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
- 1 July 2003
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 31 (13) , 3601-3604
- https://doi.org/10.1093/nar/gkg527
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.Keywords
This publication has 11 references indexed in Scilit:
- Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genesProceedings of the National Academy of Sciences, 2003
- Current methods of gene prediction, their strengths and weaknessesNucleic Acids Research, 2002
- Full-length messenger RNA sequences greatly improve genome annotationGenome Biology, 2002
- Assessment of the Total Number of Human Transcription UnitsGenomics, 2001
- GeneSplicer: a new computational method for splice site predictionNucleic Acids Research, 2001
- Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 2000
- Genie—Gene Finding in Drosophila melanogasterGenome Research, 2000
- Interpolated Markov Models for Eukaryotic Gene FindingGenomics, 1999
- Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology, 1997
- Finding Genes in DNA with a Hidden Markov ModelJournal of Computational Biology, 1997