bioinformatics

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week 7 websites

http://www.cs.jhu.edu/~salzberg/appendixa.html

http://cmgm.stanford.edu/classes/genefind/

http://linkage.rockefeller.edu/wli/gene/programs.html

http://cmgm.stanford.edu/biochem218/Projects%202002/Sen.pdf

programs that find specific types of prokaryotic sequences

BPROM http://www.softberry.com/berry.phtml?topic=bprom

NNPP / Prokaryotic http://www.fruitfly.org/seq_tools/promoter.html

TRANSTERM http://www.tigr.org/software/transterm.html

programs that find prokaryotic genes

GLIMMER http://www.tigr.org/software/glimmer/

GeneMark http://opal.biology.gatech.edu/GeneMark/

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

FGENESB http://www.softberry.com/berry.phtml?topic=fgenesb

programs that find eukaryotic promoters

http://www.fruitfly.org/seq_tools/promoter.html

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

http://www.cbil.upenn.edu/tess/

http://bimas.dcrt.nih.gov/molbio/signal/

http://argon.cshl.org/genefinder/CPROMOTER/index.htm

http://cgsigma.cshl.org/CpG_promoter/

http://rulai.cshl.org/tools/FirstEF/

http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html

http://www.itba.mi.cnr.it/webgene/

programs that find other kinds of eukaryotic sequences

http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html

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

http://argon.cshl.org/tabaska/polyadq_form.html

http://www.fruitfly.org/seq_tools/splice.html

http://www.softberry.com/berry.phtml?topic=promoter&prg=POLYAH

http://bioinformatics.iastate.edu/cgi-bin/sp.cgi

http://www.ebi.ac.uk/~thanaraj/MZEF-SPC.html

http://exon.cshl.org/ESE/

http://l25.itba.mi.cnr.it/~webgene/wwwHC_polya.html

websites that find eukaryotic genes

http://www.tigr.org/software/

http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html

http://www.softberry.com/berry.phtml?topic=gfind

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

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

http://www.fruitfly.org/seq_tools/genie.html

http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi

http://arete.ibb.waw.pl/PL/html/gene_lang.html

http://www1.imim.es/geneid.html

http://www.itba.mi.cnr.it/webgene/

Agrobacterium query

Arabidopsis query