Gene Finding and Gene Identification Resources
Owner: Pamela Shaw

Description: Servers and tools that scan a sequence for potential gene features
Know of a good resource for this list? Tell the owner

Item Description More Info
AGenDA AGenDA is a gene-prediction tool that is based on cross-species sequence comparison. The software tools CHAOS and DIALIGN are used to align a pair of syntenic genomic sequences, e.g. from human and mouse. AGenDA searches for conserved splice sites and start/stop codons at the boundaries of identified sequence homologies in order to identify potential exons. Tags Save
AMIGene AGC. AMIGene is the Annotation of Microbial Genes server. It identifies the Coding Sequences (CDSs) in a large contig or a complete bacterial genome sequence.. Tags Save
AnnotQTL Biogenoest. The AnnotQTL server is a tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region. Tags Save
Augustus: gene prediction Univ. of Gottingen. AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Tags Save
BAGEL University of Groningen. BAGEL (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Tags Save
BDGP: Neural Network Promoter Prediction Lawrence Berkeley National Laboratory. Berkeley Drosophila Genome Project. Uses neural network programming techniques to predict promoters from a submitted sequence Tags Save
CPC - Coding Potential Calculator Peking University. CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts. Tags Save
EasyGene 1.2 Server BINF, Copenhagen. EasyGene 1.2 server uses HMM to produce a list of predicted genes given a sequence of prokaryotic DNA. Tags Save
FrameD FrameD locates genes and frameshifts in procaryotic sequences and matured eukaryotic sequences (to predict and correct frameshifts in EST, EST clusters and cDNAs). Tags Save
Gene Finder Cold Spring Harbor. This page contains software tools designed to predict putative internal protein coding exons in genomic DNA sequences for humans, arabidopsis, yeast and mice. Tags Save
GeneMark Georgia Tech. The GeneMark family of programs employ Markov models for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes Tags Save
GenomeScan MIT. GenomeScan employs protein homology for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms Tags Save
GENSCAN Web Server at MIT MIT. Scans a DNA sequence for promoters and predicts gene make-up Tags Save
Glimmer Johns Hopkins Center for Computational Biology. Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Tags Save
HomoloGene NCBI. HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. Tags Save
ORF Finder NCBI. The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. Tags Save
Orphelia Orphelia is a machine learning program for metagenomic ORF finding for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin Tags Save
TACT - Transcriptome Auto-annotation Conducting Tool TACT is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predicti Tags Save