List of gene prediction software
This is a list of software tools and web portals used for gene prediction.
| Name | Description | Species | References |
| Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences | Eukaryotes | ||
| Predicting genes in complete genomes and sequencing Reads | Prokaryotes, Metagenomes | ||
| Identifies translational initiation sites in cDNA sequences | Human | ||
| 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 | ||
| Eukaryote gene predictor | Eukaryotes | ||
| BGF | Hidden Markov model 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 | |
| The gene finder is based on a hidden Markov model that is automatically estimated for a new genome. | Prokaryotes | ||
| Integrative gene finding | Prokaryotes, Eukaryotes | ||
| HMM-based gene structure prediction: multiple genes, both chains | Eukaryotes | ||
| Find genes and frameshift in G+C rich prokaryote sequences | Prokaryotes, Eukaryotes | ||
| 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 | |
| Program to predict genes, exons, splice sites, and other signals along DNA sequences | Eukaryotes | ||
| 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 | |
| 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 | |
| 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 based system to find genes | Eukaryotes | |
| mGene.ngs | SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays | Eukaryotes | |
| Decision tree system to find genes in vertebrate DNA | Eukaryotes | ||
| Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN | Prokaryotes, Eukaryotes | ||
| Neural network promoter prediction | Prokaryotes, Eukaryotes | ||
| Neural network splice site prediction | Drosophila, Human | ||
| Graphical analysis tool to find all open reading frames | Prokaryotes, Eukaryotes | ||
| Series of modular computer programs to detect regulatory signals in non-coding sequences | Fungi, Prokaryotes, Metazoa, Protist, Plants | ||
| A tool to annotate phage genomes. | Phages | ||
| SplicePredictor | Method to identify potential splice sites in pre-mRNA by sequence inspection using Bayesian statistical models | Eukaryotes | |
| VEIL | Hidden Markov model to find genes in vertebrate DNA Server | Eukaryotes |