Gene Finding Programs

This list of programs has been compiled and updated from

• James W. Fickett
Finding genes by computer: the state of the art
Trends in Genetics, August 1996, Vol 12, Num. 8, p 316-320

Tips for using these programs with a genomic sequence

•  
• 1. Remove repetitive elements (ALUs, etc.)
• 2. Perform Database Search on Translated DNA (BlastX or TFasta)
• 3. Perform ORF Gene Finding Search (Grail, GenScan, etc)
• 4. Translate putative ORFs and do Functional Analysis (Blocks, Motifs, etc)

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)