GeneFinding
From Bioinformatics.ws
| http://www.genefinding.org/ |
Description |
Contacts
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| SNAP |
GHMM eukaryotic gene finder |
Ian Korf | |
| GeneZilla (formerly TIGRscan) |
GHMM eukaryotic gene finder |
Bill Majoros |
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| GlimmerHMM | GHMM eukaryotic gene finder | Mihaela Pertea | |
| TWINSCAN | GHMM informant method for comparative gene finding | Michael Brent |
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| TWAIN |
GPHMM comparative gene finder |
Bill Majoros | |
| ExoniPhy |
Phylogenetic HMM gene finder |
Adam Siepel, David Haussler |
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| Shadower |
Generalized Hidden Markov Phylogeny (GHMP) gene finder |
Michael Jordan |
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| JIGSAW (formerly "Combiner") |
Evidence combiner for eukaryotic gene prediction |
Jonathan Allen |
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| 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 |
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| EvoGene |
Evolutionary HMM gene finder |
Jakob Pedersen |
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| ExonHunter |
Integrative gene finding system |
Broňa Brejová |
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| GlimmerM |
Eukaryotic gene finder using OC1 decision trees and Interpolated Markov Models. |
Mihaela Pertea |
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| Unveil |
HMM eukaryotic gene finder | Bill Majoros |
|
| Glimmer |
Prokaryotic gene finder using Interpolated Markov Models |
Art Delcher, Steven Salzberg |
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| CRITICA |
Comparative prokaryotic gene finder |
Jonathan Badger |
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| 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 |
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| SLAM | Pair GHMM-based syntenic gene finder | Lior Pachter |
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| EuGene | An open gene finder for eukaryotic organisms | EuGene Team |
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| GENSCAN | GHMM-based gene finder for human | Chris Burge |
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| 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 |
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| MORGAN |
A eukaryotic gene finder using OC1 decision trees (no longer supported) |
Steven Salzberg, Art Delcher |
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| GenomeScan | GHMM informant-based gene finder |
Chris Burge | |
| DoubleScan |
Pair HMM gene finder |
Irmtraud Meyer |
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| 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 |
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| Genie | GHMM-based gene finder | David Kulp, Martin Reese |
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| GeneMark(tm) | a gene finder from Georgia Institute of Technology | Mark Borodovsky | |
| FGENESH |
GHMM gene finder |
softberry@softberry.com |
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| 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 |
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| 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 |
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| 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 |
