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.

TRACTS - (Found July 2, 2008 )

TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exonintron regions and tract information.
http://bioportal.weizmann.ac.il/tracts/tracts.html

Twinscan - (Found July 2, 2008 )

Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.
http://genes.cs.wustl.edu/

Glimmer - (Found July 2, 2008 )

Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.
http://www.tigr.org/softlab/glimmer/glimmer.html

GENSCAN - (Found July 2, 2008 )

Identification of complete gene structures in genomic DNA.
http://genes.mit.edu/GENSCAN.html

GenomeScan - (Found July 2, 2008 )

Incorporates protein similarity information when predicting genes; based in part on GENSCAN.
http://genes.mit.edu/genomescan.html

AMIGene - (Found July 2, 2008 )

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.
http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

AUGUSTUS - (Found July 2, 2008 )

AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web interface, or downloaded and run locally.
http://augustus.gobics.de/submission

BAGEL - (Found July 2, 2008 )

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.
http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

BLAST - (Found July 2, 2008 )

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
http://www.ncbi.nlm.nih.gov/BLAST/

CPC - (Found July 2, 2008 )

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.
http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp