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Efficient decoding algorithms for generalized hidden Markov model gene finders
(BMC Bioinformatics, 2005-01-24)
Background: The Generalized Hidden Markov Model (GHMM) has proven a useful framework
for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and
probabilistic underpinnings. As the ...
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
(Genome Biology, 2008-01)
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool
that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM,
when combined with the Program ...
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
(Genome Biology, 2006-08-07)
Background: Predicting complete protein-coding genes in human DNA remains a significant
challenge. Though a number of promising approaches have been investigated, an ideal suite of
tools has yet to emerge that can provide ...