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 FragGeneScan Predicting genes in complete genomes and sequencing Reads Prokaryotes, MetagenomesATGpr Identifies translational initiation sites in cDNA sequences HumanProdigalIts 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) AUGUSTUS Eukaryote gene predictor Eukaryotes BGF Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program DIOGENES Fast detection of coding regions in short genome sequences Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters Vertebrates EasyGeneThe gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes EuGene Integrative gene finding Prokaryotes, Eukaryotes FGENESH HMM-based gene structure prediction: multiple genes, both chains Eukaryotes FrameD Find genes and frameshift in G+C rich prokaryote sequences Prokaryotes, Eukaryotes GeMoMa Homology-based gene prediction based on amino acid and intron position conservation as well as RNA-Seq data GENIUS II Links ORFs in complete genomes to protein 3D structures Prokaryotes, Eukaryotesgeneid Program to predict genes, exons, splice sites, and other signals along DNA sequences Eukaryotes GeneParser Parse DNA sequences into introns and exons Eukaryotes GeneMark Family of self-training gene prediction programs Prokaryotes, Eukaryotes, Metagenomes GeneTack Predicts genes with frameshifts in prokaryote genomes Prokaryotes 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 GENSCAN Predicts the locations and exon-intron structures of genes in genome sequences from a variety of organisms Vertebrate, Arabidopsis, Maize GLIMMER Finds genes in microbial DNA Prokaryotes GLIMMERHMM Eukaryotic gene-finding system Eukaryotes GrailEXP Predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repeat elements in DNA sequence Human, Mus musculus, Arabidopsis thaliana, Drosophila melanogaster mGene Support-vector machine (SVM) based system to find genes Eukaryotes mGene.ngs SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays Eukaryotes MORGAN Decision tree system to find genes in vertebrate DNA Eukaryotes BioNIX Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN Prokaryotes, Eukaryotes NNPP Neural network promoter prediction Prokaryotes, Eukaryotes NNSPLICE Neural network splice site prediction Drosophila, Human ORFfinder Graphical analysis tool to find all open reading frames Prokaryotes, Eukaryotes Regulatory Sequence Analysis Tools Series of modular computer programs to detect regulatory signals in non-coding sequences Fungi, Prokaryotes, Metazoa, Protist, Plants PHANOTATE A tool to annotate phage genomes. Phages SplicePredictor Method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models Eukaryotes VEIL Hidden Markov model to find genes in vertebrate DNA Server Eukaryotes

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

References