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. [ View Abstracts | NAR Web 2004 ]
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. [ View Abstracts | NAR Web 2006 | NAR Web 2005 | NAR Web 2004 ]
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. [ View Abstracts | NAR Web 2006 ]
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. [ View Abstracts | NAR Web 2006 | NAR Web 2004 ]
DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database. [ View Abstracts | NAR Web 2003 ]
GeneAlign is a gene prediction tool that uses conservation of gene structures and sequence homologies between protein coding regions to increase prediction accuracy. GeneAlign is currently configured to align human and mouse sequences for gene prediction. [ View Abstracts | NAR Web 2006 ]
GeneComber is an ab initio gene prediction tool developed at the UBC Bioinformatics Centre. It integrates results from two externally developed gene finders and operates on the premise that if these two gene finders agree on a prediction, we can be more confident in the prediction. [ View Abstracts ]
Incorporates protein similarity information when predicting genes; based in part on GENSCAN.
Identification of complete gene structures in genomic DNA. [ View Abstracts ]
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.
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. [ View Abstracts ]
Prediction of vertebrate and C. elegans genes. [ View Abstracts ]
Finds all open reading frames in a sequence.
SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non-coding sequences). [ View Abstracts | NAR Web 2003 ]
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. [ View Abstracts | NAR Web 2006 ]
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. [ View Abstracts | NAR Web 2006 ]
TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information. [ View Abstracts | NAR Web 2003 ]
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. [ View Abstracts ]
The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results. [ View Abstracts | NAR Web 2006 ]