Bioinformatics Links Directory : Gene Prediction

This section includes links to gene prediction programs for both eukaryotic and prokaryotic organisms. Resources that evaluate the available gene predicting programs are also included.

AGenDA - (Found July 2, 2008 )

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.
http://bibiserv.techfak.uni-bielefeld.de/agenda/

Grail - (Found July 2, 2008 )

Grail is a suite of tools which recognizes sequence features like promoters, exon candidates, simple repeats and complex repetitive elements. It also models genes based on the exon candidates.
http://compbio.ornl.gov/Grail-1.3/

HMMgene - (Found July 2, 2008 )

Prediction of vertebrate and C. elegans genes.
http://genome.cbs.dtu.dk/services/HMMgene/

ORF Finder - (Found July 2, 2008 )

Finds all open reading frames in a sequence.
http://www.ncbi.nlm.nih.gov/gorf/gorf.html

OrfPredictor - (Found July 2, 2008 )

OrfPredictor is designed for prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences.
https://fungalgenome.concordia.ca/tools/OrfPredictor.html

TACT - (Found July 2, 2008 )

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.
http://www.jbirc.aist.go.jp/tact/

TargetIdentifier - (Found July 2, 2008 )

TargetIdentifier is designed for identifying full-length EST cDNAs and functionally annotating EST cDNAs.
https://fungalgenome.concordia.ca/tools/TargetIdentifier.html

Taverna - (Found July 2, 2008 )

Taverna is a tool for creating and running bioinformatics workflows.
http://taverna.sourceforge.net/

TiCo - (Found July 2, 2008 )

TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.
http://tico.gobics.de/

TIGR Software Tools - (Found July 2, 2008 )

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).
http://www.tigr.org/software/