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]
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