# List of gene prediction software

This is a list of software tools and web portals used for gene prediction.
| Name | Description | Species |
| 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, Metagenomes |
| ATGpr | Identifies translational initiation sites in cDNA sequences | Human |
| 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) |
| 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 |
| EasyGene | The 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, Eukaryotes |
| geneid | 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 |