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Gene prediction software tools | Shotgun metagenomic sequencing data analysis

Environmental shotgun sequencing (or metagenomics) is widely used to survey the communities of microbial organisms that live in many diverse ecosystems, such as the human body. Finding the protein-coding genes within the sequences is an important…
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Glimmer
Desktop
Web

Glimmer

A system for finding genes in microbial DNA, especially the genomes of…

A system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

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Glimmer-MG
Desktop

Glimmer-MG

Allows to detect genes in environmental shotgun DNA sequences. Glimmer-MG is a…

Allows to detect genes in environmental shotgun DNA sequences. Glimmer-MG is a metagenomics gene prediction system that implements a metagenomics pipeline incorporating classification and clustering…

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GeneMark
Desktop

GeneMark

A family of gene prediction programs developed at Georgia Institute of…

A family of gene prediction programs developed at Georgia Institute of Technology.

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FragGeneScan
Desktop

FragGeneScan

A gene prediction method which combines sequencing error models and codon…

A gene prediction method which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of…

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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…

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MGA
Web
Desktop

MGA MetaGeneAnnotator

A web app and a package for gene prediction which precisely predicts all kinds…

A web app and a package for gene prediction which precisely predicts all kinds of prokaryotic genes from a single or a set of anonymous genomic sequences having a variety of lengths.…

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Orphelia
Desktop

Orphelia

A metagenomic ORF finding tool for the prediction of protein coding genes in…

A metagenomic ORF finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin.

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Plastid
Desktop

Plastid

Allows users to analyze nucleotide-resolution of genomics data. Plastid can…

Allows users to analyze nucleotide-resolution of genomics data. Plastid can extract the relevant biological information from various properties of raw read alignments. It provides consistent…

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MetaGUN
Desktop

MetaGUN

A gene prediction method for metagenomic fragments based on a machine learning…

A gene prediction method for metagenomic fragments based on a machine learning approach of SVM.

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EasyGene
Web

EasyGene

Allows automated and homogeneous annotation of protein coding genes. EasyGene…

Allows automated and homogeneous annotation of protein coding genes. EasyGene can predict the exact gene starts and has a very good combined sensitivity/specificity performance for both AT-rich and…

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Topological…
Desktop

Topological Pressure

Computes the topological pressure of a given DNA sequence with respect to a…

Computes the topological pressure of a given DNA sequence with respect to a given potential. Topological Pressure is a software package that can train on the human genome to fit the observed bin…

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MetaGenomeThrea…
Desktop

MetaGenomeThreader

Finds gene and works on metagenome sequences. MetaGenomeThreader can handle…

Finds gene and works on metagenome sequences. MetaGenomeThreader can handle short metagenome sequences with in-frame stop codons as well as frame shifts. It delivers gene predictions for a set of…

MetaGeneTack
Desktop
Web

MetaGeneTack

Addresses the challenging question of predicting frameshifts in protein-coding…

Addresses the challenging question of predicting frameshifts in protein-coding regions of metagenomic sequences without extrinsic knowledge. An advantage of ab initio approach is the ability to…

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TransGeneScan
Desktop

TransGeneScan

A software tool for finding genes in assembled transcripts from…

A software tool for finding genes in assembled transcripts from metatranscriptomic sequences. By incorporating several features of metatranscriptomic sequencing, including strand-specificity, short…

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MED
Desktop

MED

Gene prediction in prokaryotic genomes with multivariate entropy distance…

Gene prediction in prokaryotic genomes with multivariate entropy distance method.

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MGC
Desktop

MGC Metagenomic Gene Caller

A metagenomics gene caller which is based on a two-stage machine learning…

A metagenomics gene caller which is based on a two-stage machine learning approach similar to that of the state-of-the-art program Orphelia. MGC learns separate models for several pre-defined GC…

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