Software
 









Legend: =gene finder; =open source; =related program or software
 





Project



Description

Contacts


 
 

 

 



mGene


GHMM / SVM eukaryotic gene finder

Gunnar Raetsch











SNAP


GHMM eukaryotic gene finder

Ian Korf










GeneZilla (formerly TIGRscan)


GHMM eukaryotic gene finder

Bill Majoros











GlimmerHMM

GHMM eukaryotic gene finder
Mihaela Pertea










TWINSCAN

GHMM informant method for comparative gene finding
Michael Brent











ChemGenome


prokaryotic, ab initio gene finder based on physico-chemical properties

Shailesh










TWAIN


GPHMM comparative gene finder

Bill Majoros










ExoniPhy


Phylogenetic HMM gene finder

Adam Siepel, David Haussler











Shadower


Generalized Hidden Markov Phylogeny (GHMP) gene finder

Michael Jordan











JIGSAW (formerly "Combiner")


Evidence combiner for eukaryotic gene prediction

Jonathan Allen











GenomeThreader


Similarity-based gene prediction program where additional cDNA / EST and/or protein sequences are used to predict gene structures via spliced alignments.

Gordon Gremme











EvoGene


Evolutionary HMM gene finder

Jakob Pedersen











ExonHunter


Integrative gene finding system

Broňa Brejová











GlimmerM


Eukaryotic gene finder using OC1 decision trees and Interpolated Markov Models.

Mihaela Pertea











Unveil


HMM eukaryotic gene finder
Bill Majoros











Glimmer


Prokaryotic gene finder using Interpolated Markov Models

Art Delcher,
Steven Salzberg











CRITICA


Comparative prokaryotic gene finder

Jonathan Badger











SGP2


Comparative gene finder based on geneid and TBLASTX

Genis Parra, Josep F. Abril, Roderic Guigó










Phat


GHMM gene finder

Simon Cawley










geneid


Hierarchically-structured gene prediction program

Enrique Blanco, Roderic Guigó,
Genis Parra











SLAM

Pair GHMM-based syntenic gene finder
Lior Pachter











EuGene


An open gene finder for eukaryotic organisms
EuGene Team











GENSCAN

GHMM-based gene finder for human
Chris Burge











AUGUSTUS


GHMM-based gene finder for eukaryotes

Mario Stanke










SGP1


Similarity based gene prediction program

Roderic Guigó










VEIL


HMM eukaryotic gene finder (no longer supported)

John Henderson,
Steven Salzberg











MORGAN


A eukaryotic gene finder using OC1 decision trees (no longer supported)

Steven Salzberg,
Art Delcher











GenomeScan

GHMM informant-based gene finder

Chris Burge










DoubleScan


Pair HMM gene finder

Irmtraud Meyer











HMMgene

HMM gene finder
Anders Krogh Kristoffer Rapacki  










GRAIL

Neural-network-based gene-finder
grailmail@ornl.gov










GrailEXP

Neural-network-based gene finder (Oak Ridge Natl. Lab.)
feedback.cfm











Genie

GHMM-based gene finder
David Kulp,
Martin Reese











GeneMark(tm)

a gene finder from Georgia Institute of Technology
Mark Borodovsky










FGENESH


GHMM gene finder

softberry@softberry.com











ORPHEUS

bacterial gene finder

Grigori Kolesov










PROCRUSTES


gene finder utilizing protein evidence

Pavel Pevzner











Diogenes


searching for and reporting likely protein-encoding regions
John A. Crow











WebGene

Tools for prediction and analysis of protein-coding gene structure













GeneSplicer

A fast, flexible system for detecting splice sites in eukaryotic DNA.
Mihaela Pertea










ORF Finder

program at NCBI to find ORFs in a sequence
Tatiana Tatusov Roman Tatusov










SplicePredictor

a method to identify potential splice sites in (plant) pre-mRNA by sequence inspection using Bayesian statistical models












NetPlantGene

neural network predictions of splice sites in Arabidopsis thaliana DNA
Søren Brunak,
Pierre Rouze











NetGene2

neural network predictions of splice sites in human, C. elegans and A. thaliana DNA
Søren Brunak










ELPH

Gibbs sampler for finding motifs in DNA; has been used for detecting exon splice enhancers (ESE's).  Also applicable to other motif-detection tasks.
Mihaela Pertea










RBSfinder

A program to find ribosome binding sites in prokaryotic DNA.
Steven Salzberg










TransTerm

A program that finds rho-independent transcription terminators in bacterial genomes
Maria Ermolaeva










OC1

oblique decision trees for classification
Steven Salzberg,
Simon Kasif











TAIL

machine-learning library: neural nets, decision trees, multivariate regression, Bayesian classifiers, genetic algorithms/genetic programming, and K-nearest-neighbors with feature selection and correlation control
Bill Majoros










wotd


suffix trees

Stefan Kurtz










tigr++

C++ class library used by several TIGR genefinders and other packages.  Covers string & sequence processing, math/statistics, many efficient data structures, GFF parsing, sorting, and I/O.
Bill Majoros










PROSCAN/
PromoterScan


Predicts promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences
Dan Prestridge


Return to: