Table 1.

Ab initio Gene Prediction Programs (Possibly with Homology Integration)

Program	Organism	Algorithm*	Website	Homology
GeneID	Vertebrates, plants	DP	http://www1.imim.es/geneid.html
FGENESH	Human, mouse, Drosophila, rice	HMM	http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind
GeneParser	Vertebrates	NN	http://beagle.colorado.edu/~eesnyder/GeneParser.html	EST
Genie	Drosophila, human, other	GHMM	http://www.fruitfly.org/seq_tools/genie.html	protein
GenLang	Vertebrates, Drosophila, dicots	Grammar rule	http://www.cbil.upenn.edu/genlang/genlang_home.html
GENSCAN	Vertebrates, Arabidopsis, maize	GHMM	http://genes.mit.edu/GENSCAN.html
GlimmerM	Small eukaryotes, Arabidopsis, rice	IMM	http://www.tigr.org/tdb/glimmerm/glmr_form.html
GRAIL	Human, mouse, Arabidopsis, Drosophila	NN, DP	http://compbio.ornl.gov/Grail-bin/EmptyGrailForm	EST, cDNA
HMMgene	Vertebrates, C. elegans	CHMM	http://www.cbs.dtu.dk/services/HMMgene/
AUGUSTUS	Human, Arabidopsis	IMM,WWAM	http://augustus.gobics.de/
MZEF	Human, mouse, Arabidopsis, Fission yeast	Quadratic discriminant analysis	http://rulai.cshl.org/tools/genefinder/

^*DP, dynamic programming; NN, neural network; MM, Markov model; HMM, Hidden Markov model; CHMM, class HMM; GHMM, generalized HMM; IMM, interpolated MM.