List of gene prediction software

Last updated

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

NameDescriptionSpeciesReferences
FINDER Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequencesEukaryotes [1]
FragGeneScan Predicting genes in complete genomes and sequencing ReadsProkaryotes, Metagenomes [2]
ATGpr Identifies translational initiation sites in cDNA sequencesHuman [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 predictorEukaryotes [5]
BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program [6]
DIOGENESFast detection of coding regions in short genome sequences
Dragon Promoter FinderProgram to recognize vertebrate RNA polymerase II promotersVertebrates [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 findingProkaryotes, Eukaryotes [10] [11]
FGENESH HMM-based gene structure prediction: multiple genes, both chainsEukaryotes [12]
FrameD Find genes and frameshift in G+C rich prokaryote sequencesProkaryotes, Eukaryotes [13]
GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data [14] [15]
GENIUS IILinks ORFs in complete genomes to protein 3D structuresProkaryotes, Eukaryotes [16]
geneid Program to predict genes, exons, splice sites, and other signals along DNA sequencesEukaryotes [17]
GeneParser Parse DNA sequences into introns and exonsEukaryotes [18]
GeneMark Family of self-training gene prediction programsProkaryotes, Eukaryotes,

Metagenomes

 [19] [20] [21] [22]
GeneTack Predicts genes with frameshifts in prokaryote genomesProkaryotes [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 predecessorVertebrate, Arabidopsis, Maize [24]
GENSCAN Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organismsVertebrate, Arabidopsis, Maize [25] [26] [27]
GLIMMER Finds genes in microbial DNAProkaryotes [28] [29] [30]
GLIMMERHMM Eukaryotic gene-finding systemEukaryotes [31]
GrailEXPPredicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequenceHuman, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster [32] [33]
mGene Support-vector machine (SVM) based system to find genesEukaryotes [34]
mGene.ngsSVM based system to find genes using heterogeneous information: RNA-seq, tiling arraysEukaryotes [35]
MORGAN Decision tree system to find genes in vertebrate DNAEukaryotes [36]
BioNIX Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCANProkaryotes, Eukaryotes [37]
NNPP Neural network promoter predictionProkaryotes, Eukaryotes [38]
NNSPLICE Neural network splice site predictionDrosophila, 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 sequencesFungi, Prokaryotes, Metazoa, Protist, Plants [41] [42]
PHANOTATE A tool to annotate phage genomes.Phages [43]
SplicePredictorMethod to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical modelsEukaryotes [44]
VEIL Hidden Markov model to find genes in vertebrate DNA ServerEukaryotes [45]

See also

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References

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