GeneFinding

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http://www.genefinding.org/
Description
Contacts

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

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
Bro┼ła 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 TatusovRoman 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

 

 

  
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