Gene Finding Programs


This list of programs has been compiled and updated from

Tips for using these programs with a genomic sequence

Always have more than one program analyze your data.


Category

Service

Organism(s)

Address

Repeat Analysis

Pythia
give a list of repeats in sequence

Human
and others

ftp://ncbi.nlm.nih.gov/repository/rebase/REF

Repeat Analysis

Repbase
repeat collections

Human

pythia@anl.gov

Repeat Analysis

BLASTX
tools to mask repeat
occurrences

Any

http://www.ncbi.nlm.nih.gov/BLAST/

Database Search

BLAST

Any

http://www.ncbi.nlm.nih.gov/BLAST

Database Search

FASTA
TFASTA

Any

Local Search with GCG

Database Search

BLOCKS
Search for functional motifs

Any

http://www.blocks.fhcrc.org/

Database Search

ProfileScan

Any

http://ulrec3.unil.ch/software/PFSCAN_form.html

Database Search

MotifFinder

Any

motif@genome.ad.jp

Gene Identification

FGENEH
integrated method

Human

service@theory.bchs.uh.edu

Gene Identification

GeneID
integrated method

Vertebrate

geneid@bir.cedb.uwf.edu

Gene Identification

GeneMark
coding region

Many

genemark@ford.gatech.edu

Gene Identification

GenLang
Integrated method

Dicots, Drosophila
vertebrates

http://cbil.humgen.upenn.edu/~sdong/genlang_home.html

Gene Identification

GenParser
Integrated method

Human

http://beagle.colorado.edu/~eesnyder/GeneParser.html

Gene Identification
The Stanford Way

GenScan
Integrated method

Vertebrates
Plants

http://genes.mit.edu/GENSCAN.html

Gene Identification

GRAIL
integrated method

Human

http://grail.lsd.ornl.gov/grailexp/

Gene Identification

EcoParse
integrated method

E. coli

ecoparse@cse.ucsc.edu

Gene Identification

GeneFinder

Any

http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html

Gene Identification

ORF Finder

Any

http://www.ncbi.nlm.nih.gov/gorf/gorf.html

Signal Recognition

PromoterScan

Eukaryotes

http://bimas.dcrt.nih.gov/molbio/proscan/index.html

Signal Recognition

NetGene

Human

netgene@virus.fki.dth.dk

Integrated Analysis

Search Launcher

Any

http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html

Split Gene Analysis

Pointers to other sites

Any

http://gnomic.stanford.edu/~volker/splitgenes.html

Signal Recognition

PatScan

Any

http://www.mcs.anl.gov/home/papka/ROSS/patscan.html

Gene Mark Help

GeneMark Help

http://www.microbiology.adelaide.edu.au/links/genemark.htm

Signal Recognition

FINEX - Fingerprinting of Intron Exon Boundaries

Many

http://www.biu.icnet.uk/projects/finex/

Gene Identification

PROCRUSTES

Many

http://www-hto.usc.edu/software/procrustes/

Signal Recognition

GenQuest

Many

http://www.gdb.org/Dan/gq/gq.form.htm

Gene Identification

CBS -Denmark

Human & Arabidopsis

http://www.cbs.dtu.dk/services/

Gene Identification

ORPHEUS

Bacterial

http://pedant.mips.biochem.mpg.de/frishman/orpheus_home.html

Hidden Markov

FGENESH+

Human, Drosophila, Nematode and Plant

http://genomic.sanger.ac.uk/

Documentation for the email services can be obtained by sending a message with only the word

help

in the body of the message. Don't have a subject line, and no signature.

For more information, check out Pedro's List of Biological Web Sites

Lots more Links to Genome Information

Structural Classification of Proteins (SCOP)




Lee Kozar / Manager, Bioinformatics Resource / lkozar@cmgm.stanford.edu