DNA
functional site miner (DNAFSMiner)
- contains two software tools: TIS Miner which can be used
to predict translation initiation site (TIS) in vertebrate mRNA, cDNA, or DNA
sequences. The other is called Poly(A)
Signal Miner which can be used to predict polyadenylation (poly(A)) signal in
human DNA sequences (Reference: H. Liu, et al. (2005) Boinformatics 21: 671-673.
FirstEF (R.
Davuluri, I. Grosse, & M. Zhang, Cold Sring Harbor Laboratory, U.S.A.) is
a first-exon and promoter prediction program
for human
DNA.
AUGUSTUS -
uses gene prediction in eukaryotic (Human, Drosophila, Arabidopsis, Brugia, Aedes, Coprinus, &
Tribolium)
sequences that is based on a generalized hidden Markov
model, a probabilistic model of a sequence and its
gene structure.
The web server allows the user to impose constraints on the predicted
gene structure (Reference: M.
Stanke & B. Morgenstern. 2005. Nucl. Acids Res. 33: W465-W467).
TWINSCAN (M.Brent, Computational Genomics Group,
Washington University, U.S.A.) - I am particularly
impressed with the
output which
provides
one with the location of the exons, a
trimmed ORF and the protein sequence linked to BLASTN
& P searches.
Can be used
for analysis
of mammalian (human and non-human), plant (Arabidopsis and
non-
Arabidopsis dicots), worm (Caenorhabditis elegans)
and fungus
(Cryptococcus neoformans) gene analysis.
GENSCAN (C. Burge, Massachusetts Institute of Technology,
U.S.A.) can be accessed via the MIT Server or the Pasteur
Institute
Server.
GenomeScan
(C. Burge, MIT, U.S.A.) -
The newer version of GENSCAN this can be used to predict vertebrate,
Arabidopsis &
maize
genes.
GeneMark (European Bioinformatics Institute,
United Kingdom) - offers plenty of model systems (A.
thaliana, C. elegans, D.
melanogaster, G. gallus, H. sapiens, F. rubrupes,
M. musculus, R. norvegicus and S. cerevisiae) with many options.
GlimmerM (The
Institute for Genomic Research) - provides the
following model organisms: Arabidopsis,Aspergillus,
Brugia,
Cryptococcus, Entamoeba, Oryza, Plasmodium, Schistosoma and Theileria.
Accepts 31kb by pasting
and 200kb by uploading.
Genome Analysis Pipeline (Genome Analysis
and System Modeling Group, Life Sciences Division, Oak Ridge National
Laboratory, U.S.A.) -
offers both prokaryote
(Generation and Glimmer) as well as
higher
eukaryotes and Saccharomyces
(GrailEXP and Genscan)
genome
analysis. One
also has the option of
choosing "Select all services". Very nice
Java and html presentation
of analysis results.
FGENESH (SoftBerry)
- very fast HMM-based gene structure prediction program.
geneid
(Genome Informatics Research Lab, Universitat Pompeu Fabra, Spain) -
Prediction of human
& Drosophila genes.
GenLang
(University of Pennsylvania, Computational Biology and
Informatics Laboratory, U.S.A.) - Prediction of vertebrate,
Drosophila and
dicot genes.
HMMgene
(Anders Krogh, Center for Biological Sequence Analysis,
Denmark) - Prediction of vertebrate and C.
elegans genes.
NetPlantGene (Center for Biological Sequence Analysis,
Denmark) - neural network predictions of splice sites in
Arabidopsis thaliana
DNA.
Genie: (Berkeley Drosophila Genome Project, U.S.A.)
- Gene finder based upon generalized Hidden Markov Models.
Human & Drosophila
genes.
GeneSeqer
(Bioinformatics, Computational Biology, and Biological Statistics,
Iowa State University, U.S.A.) - select either
human, mouse, rat,
chicken, Drosophila, nematode, yeast, Aspergillus,
Arabidopsis [default], or
maize.
GrailEXP
(Computational Biology Program, Oak Ridge National
Laboratory, U.S.A.) - human, mouse,
Arabidopsis,
maize plus many options.
GeneWalker
(Japan Science and Technology Corporation)
FrameD
- is a A noise-resistant gene finder for prokaryotic and matured
eukaryotic sequences offering considerable flexibility in search strategies and
output format (Reference: Schiex, T. et al. 2003.
Nucl. Acids. Res. 31: 3738-374).
SplicePort
— An interactive splice-site analysis tool (Reference: R.I. Dogan et al. 2007. Nucl. Acids Res.
35: W285-W291). Your might want to try the site out
with Mus musculus PLRLC-C mRNA for myosin light chain 2 (X65981 ).
An alternative:
GeneMachine
(I. Makalowska, J. F. Ryan, & A.D. Baxevanis; Genome Technology Branch, National Human Genome
Research Institute, National
Institutes of
Health,
U.S.A.) is a suite of Perl programs and modules used to run
MZEF,
GENSCAN, GRAIL2, FGENES, RepeatMasker,
Sputnik,
BLASTX and BLASTN. N.B. You have to register to a free account.