FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.
We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.
Schiex
Thomas
T
Unité de Biométrie et Intelligence Artificielle, INRA, CNRS-INRA, 31326, Castanet Tolosan Cedex, France. tschiex@toulouse.inra.fr
Gouzy
Jérôme
J
Moisan
Annick
A
de Oliveira
Yannick
Y
D003196:Computer Graphics; D018076:DNA, Complementary / Q000737:chemistry; D005057:Eukaryotic Cells; D020224:Expressed Sequence Tags; D016368:Frameshift Mutation; D020862:GC Rich Sequence; D005796:Genes; D016680:Genome, Bacterial; D020407:Internet; D016366:Open Reading Frames; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid; D012984:Software
D018076:DNA, Complementary