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Protein-coding gene detection software tools | Genome annotation

Accurate gene structure prediction plays a fundamental role in functional annotation of genes. The main focus of gene prediction methods is to find patterns in long DNA sequences that indicate the presence of genes. Source text: Al-Turaiki et al.,…
GENSCAN
Web

GENSCAN

Identifies complete exon/intron structures of genes in genomic DNA. GENSCAN…

Identifies complete exon/intron structures of genes in genomic DNA. GENSCAN uses a homogeneous fifth order Markov model of noncoding regions and a three periodic (inhomogeneous) fifth order Markov…

Twinscan/N-SCAN
Web

Twinscan/N-SCAN

A software tool for gene-structure prediction. N-SCAN can model the…

A software tool for gene-structure prediction. N-SCAN can model the phylogenetic relationships between the aligned genome sequences, context dependent substitution rates, and insertions and…

FGENESH
Web

FGENESH

A program for predicting multiple genes in genomic DNA sequences. FGENESH was…

A program for predicting multiple genes in genomic DNA sequences. FGENESH was selected as the most accurate program for plant gene identification.

CESAR
Desktop

CESAR Coding Exon Structure Aware Realigner

Avoids spurious mutations while being able to report real mutations, both on…

Avoids spurious mutations while being able to report real mutations, both on simulated and real data. CESAR is an Hidden-Markov-Model (HMM) based method that enhances the utility of genome alignments…

G T A T C G C T A
Prodigal
Desktop

Prodigal PROkaryotic DYnamic programming Gene-finding ALgorithm

A gene-finding program for microbial genomes. The goals of Prodigal were to…

A gene-finding program for microbial genomes. The goals of Prodigal were to attain greater sensitivity in identifying existing genes, to predict translation initiation sites more accurately, and to…

HMMgene
Web

HMMgene

Prediction of vertebrate and C. elegans genes. HMMGene is based on a…

Prediction of vertebrate and C. elegans genes. HMMGene is based on a probabilistic model called a hidden Markov model, and the probabilistic framework facilitates the inclusion of database matches of…

GlimmerHMM
Desktop

GlimmerHMM

A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the…

A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models…

GeMoMa
Web
Desktop

GeMoMa Gene Model Mapper

A homology-based gene prediction program. GeMoMa utilizes the conservation of…

A homology-based gene prediction program. GeMoMa utilizes the conservation of intron positions within genes to predict related genes in other organisms. We assess the performance of GeMoMa and…

COGNATE
Desktop

COGNATE Comparative Gene Annotation characterizer

Analyze simultaneously a given protein-coding gene annotation and the…

Analyze simultaneously a given protein-coding gene annotation and the corresponding assembled sequences of a genome. COGNATE is a tool that allows a quick and easy extraction of basic genome feature…

IPred
Desktop

IPred Integrative gene Prediction

A method to integrate ab initio and evidence based gene identifications to…

A method to integrate ab initio and evidence based gene identifications to complement the advantages of different prediction strategies. IPred builds on the output of gene finders and generates a new…

ALNGG
Web
Desktop

ALNGG

Allows detection of the protein coding gene by comparing genome between two…

Allows detection of the protein coding gene by comparing genome between two species. ALNGG directly compares two full sets of mammalian chromosomes and automatically identify protein-coding exons on…

G T A T C G C T A
DOGMA
Desktop

DOGMA DOmain-based General Measure for transcriptome and proteome quality Assessment

A program for fast and easy quality assessment of transcriptome and proteome…

A program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides…

GeneWise
Web
Desktop

GeneWise

Predicts gene structure using similar protein sequences. GeneWise is heavily…

Predicts gene structure using similar protein sequences. GeneWise is heavily used by the Ensembl annotation system. It was developed from a principled combination of hidden Markov models (HMMs).…

GenomeScan
Web

GenomeScan

A gene identification algorithm that combines exon-intron and splice signal…

A gene identification algorithm that combines exon-intron and splice signal models with similarity to known protein sequences in an integrated model. GenomeScan can accurately identify the…

GeneID
Desktop

GeneID

Predicts genes in anonymous genomic sequences designed with a hierarchical…

Predicts genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using…

CRITICA
Desktop

CRITICA Coding Region Identification Tool Invoking Comparative Analysis

A microbial gene finder that combines traditional approaches to the problem…

A microbial gene finder that combines traditional approaches to the problem with a novel comparative analysis. In the comparative component of the analysis, regions of DNA are aligned with related…

mGene.web
Desktop
Web

mGene.web

A web service for the genome-wide prediction of protein coding genes from…

A web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. mGene.web offers pre-trained models for the recognition of gene structures including untranslated…

JIGSAW
Desktop

JIGSAW

A gene finding system designed to automate the process of predicting gene…

A gene finding system designed to automate the process of predicting gene structure from multiple sources of evidence, with results that often match the performance of human curators. JIGSAW computes…

SinEx DB
Dataset

SinEx DB

Permits users to address questions regarding the occurrence, genomic and…

Permits users to address questions regarding the occurrence, genomic and functional distribution of single exon genes (SEGs) on a large comparative genome scale. SinEx DB can be useful for generating…

Seqping
Desktop

Seqping

An automated pipeline that performs gene prediction using self-trained HMM…

An automated pipeline that performs gene prediction using self-trained HMM models and transcriptomic data. The program processes the genome and transcriptome sequences of a target species through…

NPACT
Desktop
Web

NPACT N-Profile Analysis Computational Tool

A computational and graphical representation tool for gene identification and…

A computational and graphical representation tool for gene identification and sequence annotation. NPACT identifies sequence segments of any length with statistically-significant 3-base compositional…

SGP2
Desktop

SGP2

A method to predict genes in a target genome sequence using the sequence of a…

A method to predict genes in a target genome sequence using the sequence of a second informant or reference genome. Essentially, SGP2 is a framework to integrate the ab initio gene prediction program…

Rosetta
Desktop

Rosetta

Predicts coding exons on a target human sequence (may also work for other…

Predicts coding exons on a target human sequence (may also work for other mammalian sequences as targets), based on comparison with a homologous sequence from a different species. Rosetta identifies…

AnABlast
Desktop

AnABlast Ancestral-patterns search through A BLAST-based strategy

Generates profiles of accumulated alignments in query amino acid sequences…

Generates profiles of accumulated alignments in query amino acid sequences using a low-stringency BLAST strategy. To validate this approach, all six-frame translations of DNA sequences between every…

ExonHunter
Desktop

ExonHunter

A eukaryotic gene finder that can use multiple sources of evidence to improve…

A eukaryotic gene finder that can use multiple sources of evidence to improve prediction accuracy. ExonHunter is based on hidden Markov models allowing use of variety of additional sources of…

FrameD
Desktop
Web

FrameD

A program that predicts coding regions in prokaryotic and matured eukaryotic…

A program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows…

OrthoFiller
Desktop

OrthoFiller

Leverages information from multiple related species to identify those genes…

Leverages information from multiple related species to identify those genes whose existence can be verified through comparison with known gene families, but which have not been predicted. OrthoFiller…

BASID2CS
Dataset

BASID2CS BASID2CS: The basidiomycetes Two Componen Systems repository

A pipeline web server that extends the analysis to the complete genome…

A pipeline web server that extends the analysis to the complete genome sequences of basidiomycetes. BASID2CS has been specifically designed for the identification, classification and functional…

RescueNet
Desktop

RescueNet RElative Synonymous Codon Usage Neural Network

Identifies automatically multiple gene models within a genome. RescueNet uses…

Identifies automatically multiple gene models within a genome. RescueNet uses relative synonymous codon usage as the indicator of protein-coding potential. It identifies some genes that other methods…

AUGUSTUS
Desktop
Web

AUGUSTUS

Predicts genes in eukaryotic genomic sequences. AUGUSTUS is based on the…

Predicts genes in eukaryotic genomic sequences. AUGUSTUS is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both…

EuGene
Desktop

EuGene

An open integrative gene finder for eukaryotic and prokaryotic genomes.…

An open integrative gene finder for eukaryotic and prokaryotic genomes. Compared to most existing gene finders, EuGene is characterized by its ability to simply integrate arbitrary sources of…

TWAIN
Desktop

TWAIN

Employs a Generalized Pair Hidden Markov Model (GPHMM) to predict genes in two…

Employs a Generalized Pair Hidden Markov Model (GPHMM) to predict genes in two closely related eukaryotic genomes simultaneously. TWAIN utilizes the MUMmer package to perform approximate alignment…

GeneZilla
Desktop

GeneZilla

A state-of-the-art gene finder based on the Generalized Hidden Markov Model…

A state-of-the-art gene finder based on the Generalized Hidden Markov Model framework, similar to Genscan and Genie. GeneZilla is highly reconfigurable and includes software for retraining by the…

Chemgenome
Desktop
Web

Chemgenome

An ab-intio gene prediction software, which find genes in prokaryotic genomes…

An ab-intio gene prediction software, which find genes in prokaryotic genomes in all six reading frames. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic…

FEX
Web

FEX

Finds potential 5'-, internal and 3'-coding exons. FEX uses a linear…

Finds potential 5'-, internal and 3'-coding exons. FEX uses a linear discriminant function to combine characteristics describing donor and acceptor splice sites, 5'- and 3'-intron…

CONSORF
Web

CONSORF

A fully automatic high-accuracy identification system that provides consensus…

A fully automatic high-accuracy identification system that provides consensus prokaryotic CDS information. CONSORF first predicts the CDSs supported by consensus alignments. The alignments are…

genBlastG
Desktop
Web

genBlastG

Constructs the gene models directly from the high-scoring segment pairs…

Constructs the gene models directly from the high-scoring segment pairs returned by BLAST, with the intention of leveraging the wide success of BLAST. genBlastG can find gene models much faster than…

Doublescan
Web

Doublescan

A program for comparative ab initio prediction of protein coding genes in mouse…

A program for comparative ab initio prediction of protein coding genes in mouse and human DNA. Doublescan takes two input DNA sequences (one from mouse, one from human) which are known to be or which…

GrailEXP
Desktop

GrailEXP Gene Recognition and Analysis Internet Link

A widely used systems for evaluating the protein-coding potential of anonymous…

A widely used systems for evaluating the protein-coding potential of anonymous DNA sequences. GrailEXP predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements…

SNAP
Desktop

SNAP Semi-HMM-based Nucleic Acid Parser

Computational gene prediction continues to be an important problem, especially…

Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. SNAP is a general purpose gene finding program suitable for both eukaryotic…

GenomeThreader
Desktop

GenomeThreader

A software tool to compute gene structure predictions. The gene structure…

A software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to…

Genie
Web

Genie

A software tool based on a generalized Hidden Markov Model (GHMM) that…

A software tool based on a generalized Hidden Markov Model (GHMM) that describes the grammar of a legal parse of a multi-exon gene in a DNA sequence. In Genie, probabilities are estimated for gene…

PASA
Desktop

PASA Program to Assemble Spliced Alignments

Allows automation improvement of gene structures in Arabidopsis thaliana. PASA…

Allows automation improvement of gene structures in Arabidopsis thaliana. PASA was used in Eukaryotic genome annotation projects such as Rice, Aspergillus species, Plasmodium falciparum, Schistosoma…

BESTORF
Web

BESTORF

Finds potential coding fragment EST/mRNA. BESTORF is based on Markov chain…

Finds potential coding fragment EST/mRNA. BESTORF is based on Markov chain model of coding regions and can combine it with Start codon potential thank to a probabilistic model. It returns potential…

AMARE
Desktop

AMARE

Optimizes the signal-to-noise ratio in amplified fragment-length polymorphism…

Optimizes the signal-to-noise ratio in amplified fragment-length polymorphism (AFLP) data sets (single or multiple primer combinations). AMARE identifies potentially erroneous AFLP genotyping errors…

tcode
Desktop

tcode

Identifies protein-coding regions using Fickett TESTCODE statistic. tcode…

Identifies protein-coding regions using Fickett TESTCODE statistic. tcode identifies protein-coding regions in one or more DNA sequences. It is based on simple and universal differences between…

Phat
Desktop

Phat Pretty handy annotation tool

A program for finding genes in eukaryotic organisms. Phat was originally…

A program for finding genes in eukaryotic organisms. Phat was originally developed with a view to annotating Plasmodium falciparum data but now comes with code to retrain it for other organisms. It…

BGF
Web

BGF Beijing Gene Finder

With several rice genome projects approaching completion gene…

With several rice genome projects approaching completion gene prediction/finding by computer algorithms has become an urgent task. BGF is an ab initio gene prediction program.

ZCURVE
Web

ZCURVE

An ab initio program for gene finding in bacterial or archaeal genomes. Based…

An ab initio program for gene finding in bacterial or archaeal genomes. Based on cross validations of 422 prokaryotic genomes, ZCURVE 3.0 has slightly higher accuracy than Glimmer 3.02. As the most…

SLAM
Desktop

SLAM

A probabilistic framework for gene structure and alignment that can be used to…

A probabilistic framework for gene structure and alignment that can be used to simultaneously find both the gene structure and alignment of two syntenic genomic regions. A key feature of the method…

GeneMapper
Desktop

GeneMapper

A flexible genotyping software package that provides DNA sizing and quality…

A flexible genotyping software package that provides DNA sizing and quality allele calls for all Life Technologies® electrophoresis-based genotyping systems. GeneMapper specializes in…

Projector
Web

Projector

A program for the comparative, homology based prediction of protein coding…

A program for the comparative, homology based prediction of protein coding genes in mouse and human DNA. Projector takes the known genes of one DNA sequence and predicts the corresponding genes in an…

EvoGene
Desktop

EvoGene

An Evolutionary Hidden Markov Model (EHMM), being composed of an HMM and a set…

An Evolutionary Hidden Markov Model (EHMM), being composed of an HMM and a set of region-specific evolutionary models based on a phylogenetic tree. All parameters can be estimated by maximum…

shadower
Web

shadower

A formal probabilistic framework for combining phylogenetic shadowing with…

A formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a…

ESTMAP
Web

ESTMAP

Utilizes homology searches against a database of repetitive elements using the…

Utilizes homology searches against a database of repetitive elements using the RepeatView program and the expressed sequence tag (EST). Division of GenBank using the BLASTN program. ESTMAP extracts…

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