List of gene prediction software - AbsoluteAstronomy.com

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

Gene prediction

In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions...

Ab initio approaches

Name	Description	Links	References
ATGpr	identifying translational initiation sites in cDNA sequences
AUGUSTUS Augustus Augustus ;23 September 63 BC – 19 August AD 14) is considered the first emperor of the Roman Empire, which he ruled alone from 27 BC until his death in 14 AD.The dates of his rule are contemporary dates; Augustus lived under two calendars, the Roman Republican until 45 BC, and the Julian...	predicts genes in eukaryotic genomic sequences	webserver
BGF	hidden Markov model (HMM) Hidden Markov model A hidden Markov model is a statistical Markov model in which the system being modeled is assumed to be a Markov process with unobserved states. An HMM can be considered as the simplest dynamic Bayesian network. The mathematics behind the HMM was developed by L. E... and dynamic programming Dynamic programming In mathematics and computer science, dynamic programming is a method for solving complex problems by breaking them down into simpler subproblems. It is applicable to problems exhibiting the properties of overlapping subproblems which are only slightly smaller and optimal substructure... based ab initio gene prediction program
DIOGENES Diogenes Diogenes is a Greek name shared by several important historical figures:*Diogenes of Sinope , better known as Diogenes the Cynic or simply Diogenes, philosopher...	a system for fast detection of coding regions in short genomic sequences
Dragon Promoter Finder	software for recognition of vertebrate RNA Polymerase II promoters
EUGENE	gene finding for Arabidopsis thaliana
FRAMED Framed As a proper noun, Framed can refer to:Framed, 1930 film starring Regis ToomeyFramed, 1947 film noir starring Glenn Ford*Framed, 1975 film starring Joe Don Baker...	find genes and frameshift in G+C rich GC-content In molecular biology and genetics, GC-content is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine . This may refer to a specific fragment of DNA or RNA, or that of the whole genome... prokaryotic Prokaryote The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles... sequences	webserver
GENIUS Genius Genius is something or someone embodying exceptional intellectual ability, creativity, or originality, typically to a degree that is associated with the achievement of unprecedented insight....	linking ORFs in complete genomes to protein 3D structures
GENEID	program to predict genes, exons, splice sites and other signals along a DNA sequence
GENEPARSER	Parse a DNA sequence into introns and exons
GeneMark GeneMark GeneMark is a family of gene prediction programs developed at the Georgia Institute of Technology in Atlanta. First developed in 1993, GeneMark was the first gene finding method recognized as an efficient and accurate tool for genome projects...	family of gene prediction programs	webserver
GeneMark.hmm GeneMark GeneMark is a family of gene prediction programs developed at the Georgia Institute of Technology in Atlanta. First developed in 1993, GeneMark was the first gene finding method recognized as an efficient and accurate tool for genome projects...	gene prediction program for prokaryotes and eukaryotes	webserver
GeneTack	prediction of genes with frameshifts in prokaryotic genomes	webserver
NIX Nix The Neck/Nixie are shapeshifting water spirits who usually appear in human form. The spirit has appeared in the myths and legends of all Germanic peoples in Europe....	web tool for combining results from different programs (GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN)
GLIMMER Glimmer GLIMMER was the first bioinformatics system for finding genes that used the interpolated Markov model formalism. It is very effective at finding genes in bacteria, archaea, and viruses, typically finding 98–99% of all protein-coding genes. The GLIMMER software is open source and can be...	finding genes in microbial DNA	sourcecode webserver
VEIL	hidden markov model for finding genes in vertebrate DNA Server
MORGAN Morgan -Places:AustraliaMorgan, South AustraliaCanadaMorgan, OntarioUnited StatesMorgan, CaliforniaMorgan, GeorgiaMorgan, MinnesotaMorgan, TexasMorgan, UtahMorgan, Vermont*Morgan, Wisconsin, a town...	a decision tree system for finding genes in vertebrate DNA
SPLICEPREDICTOR	a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models
GENESCAN	finding genes using Fourier transform
NNPP	promoter prediction by neural network
NNSPLICE	splice site prediction by neural network
Regulatory Sequence Analysis Tools	provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.
GENOMESCAN	predicts locations and exon-intron structures of genes in genomic sequences from a variety of organisms.	webserver
ORF FINDER	a graphical analysis tool which finds all open reading frames
GrailEXP	predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements within DNA sequence

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