List of gene prediction software

This is a list of software tools and web portals used for gene prediction.

Name	Description	Species	References
FINDER	Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences	Eukaryotes	[1]
FragGeneScan	Predicting genes in complete genomes and sequencing Reads	Prokaryotes, Metagenomes	[2]
ATGpr	Identifies translational initiation sites in cDNA sequences	Human	[3]
Prodigal	Its name stands for Prokaryotic Dynamic Programming Genefinding Algorithm. It is based on log-likelihood functions and does not use Hidden or Interpolated Markov Models.	Prokaryotes, Metagenomes (metaProdigal)	[4]
AUGUSTUS	Eukaryote gene predictor	Eukaryotes	[5]
BGF	Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program		[6]
DIOGENES	Fast detection of coding regions in short genome sequences
Dragon Promoter Finder	Program to recognize vertebrate RNA polymerase II promoters	Vertebrates	[7]
EasyGene	The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome.	Prokaryotes	[8][9]
EuGene	Integrative gene finding	Prokaryotes, Eukaryotes	[10][11]
FGENESH	HMM-based gene structure prediction: multiple genes, both chains	Eukaryotes	[12]
FrameD	Find genes and frameshift in G+C rich prokaryote sequences	Prokaryotes, Eukaryotes	[13]
GeMoMa	Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data		[14][15]
GENIUS II	Links ORFs in complete genomes to protein 3D structures	Prokaryotes, Eukaryotes	[16]
geneid	Program to predict genes, exons, splice sites, and other signals along DNA sequences	Eukaryotes	[17]
GeneParser	Parse DNA sequences into introns and exons	Eukaryotes	[18]
GeneMark	Family of self-training gene prediction programs	Prokaryotes, Eukaryotes, Metagenomes	[19][20][21][22]
GeneTack	Predicts genes with frameshifts in prokaryote genomes	Prokaryotes	[23]
GenomeScan	Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms, GENSCAN server is the GenomeScan's predecessor	Vertebrate, Arabidopsis, Maize	[24]
GENSCAN	Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms	Vertebrate, Arabidopsis, Maize	[25][26][27]
GLIMMER	Finds genes in microbial DNA	Prokaryotes	[28][29][30]
GLIMMERHMM	Eukaryotic gene-finding system	Eukaryotes	[31]
GrailEXP	Predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequence	Human, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster	[32][33]
mGene	Support-vector machine (SVM) based system to find genes	Eukaryotes	[34]
mGene.ngs	SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays	Eukaryotes	[35]
MORGAN	Decision tree system to find genes in vertebrate DNA	Eukaryotes	[36]
BioNIX	Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN	Prokaryotes, Eukaryotes	[37]
NNPP	Neural network promoter prediction	Prokaryotes, Eukaryotes	[38]
NNSPLICE	Neural network splice site prediction	Drosophila, Human	[39]
ORFfinder	Graphical analysis tool to find all open reading frames	Prokaryotes, Eukaryotes	[40]
Regulatory Sequence Analysis Tools	Series of modular computer programs to detect regulatory signals in non-coding sequences	Fungi, Prokaryotes, Metazoa, Protist, Plants	[41][42]
PHANOTATE	A tool to annotate phage genomes.	Phages	[43]
SplicePredictor	Method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models	Eukaryotes	[44]
VEIL	Hidden Markov model to find genes in vertebrate DNA Server	Eukaryotes	[45]

See also

• Gene prediction
• List of RNA structure prediction software
• Comparison of software for molecular mechanics modeling