Prediction Informatics Resources At TIGR & Elsewhere

OVERVIEW

This page is intended to act as a repository for all of our software, documentation, experimental results, and "tips, tricks, & lessons learned" for gene-finding in particular and bioinformatics prediction problems in general. Included are full source code for all TIGR gene-finders as well as C++ class libraries and other components for prediction and machine learning tasks.

Source Code -- Complete Projects

Project

Description

Language

TigrScan

GHMM gene-finder like Genscan/Genie written in highly optimized C++ & designed to be extensible and reusable for other tasks related to gene-finding.

C++

GlimmerHMM

GHMM gene-finder like Genscan/Genie, written in C. Very fast and accurate.

Combiner

GlimmerM

Unveil

Pure HMM-based gene-finder based on the VEIL model. Highly optimized C++.

C++

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.

GeneSplicer

Glimmer

TransTerm

RBSfinder

VEIL

The original VEIL gene-finder.

C++

MORGAN

All of the software listed above is Open Source and is distributed under the ARTISTIC LICENSE. See www.opensource.org.

Source Code -- Reusable Software Components

Package

Description

Language

OC1

oblique decision trees for classification

NET

backpropagation neural networks for classification

C++

entropy-based decision trees for classification

C++

Suffix Trees

Suffix trees by Stephan Kurtz

tigr++

C++ container 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.

C++

regress

multivariate regression for classification

C++

bayes

Naive Bayes classifier

C++

genetic algorithms / genetic programming

C++

KNN

K-nearest-neighbors classifier with Mahalanobis distance (to control for correlation among attributes) and feature selection based on F-ratio.

C++

All of the software listed above is Open Source and is distributed under the ARTISTIC LICENSE. See www.opensource.org.

Documentation
TigrScan User Manual	How to install and use the TigrScan gene-finder
TigrScan Training Manual	How to train the TigrScan gene-finder
TigrScan Software Architecture	How the TigrScan gene-finder software is structured -- for those who wish to modify the program

Training Data
Arabidopsis.thaliana.tar.gz	GFF coordinates & FASTA file
Aspergillus.fumigatus.tar.gz	GFF coordinates & FASTA file
Aspergillus.spp.tar.gz	GFF coordinates & FASTA file
Homo.sapiens.tar.gz	GFF coordinates & FASTA file
Mus.musculus.tar.gz	GFF coordinates & FASTA file
Plasmodium.falciparum.tar.gz	GFF coordinates & FASTA file
ml-training-sets.tar.gz	sample training/test/configuration files for machine-learning packages

Experimental Results
description	poster	date
comparison of machine learning methods for discriminating exons from non-exon ORFs	bmajoros	1-19-04

External Links
Link	Description
GFF	general Feature Format definition at the Sanger center
ORF Finder	program at NCBI to find ORFs in a sequence
GenomeScan	Pair HMM
HMMgene
WebGene
SplicePredictor
GRAIL	Neural-network-based gene-finder
NetPlantGene
TWINSCAN	GHMM "informant" method
GeneMark(tm)	a gene finder from Georgia Institute of Technology
Bibliography	Bibliography on Computational Gene Recognition
GENSCAN	GHMM-based gene-finder for human
SLAM	Pair GHMM-based syntenic gene-finder
EuGene
Genie	GHMM-based gene-finder
NetGene2
GrailEXP	Neural-network-based gene-finder

TIGR assumes no responsibility for the content of the pages linked in this table.