博文
寻找启动子的工具
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一、数据库
https://blog.sciencenet.cn/blog-247480-483245.html
上一篇：mRNA序列、cDNA序列、ORF序列、CDS序列、Promoter、STS、ETS
下一篇：唐僧西天取经每天走了多少步
UCSC: http://genome.ucsc.edu/
TFD: http://www.ifti.org/
TRRD: http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
TransFac: http://www.gene-regulation.com/
Jaspar: http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl
dbTSS: http://dbtss.hgc.jp/
PlantCare: http://oberon.fvms.ugent.be:8080/PlantCARE/index.html
PLACE: http://www.dna.affrc.go.jp/htdocs/PLACE/
PlantPromDB: http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
TRRD: http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
TransFac: http://www.gene-regulation.com/
Jaspar: http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl
dbTSS: http://dbtss.hgc.jp/
PlantCare: http://oberon.fvms.ugent.be:8080/PlantCARE/index.html
PLACE: http://www.dna.affrc.go.jp/htdocs/PLACE/
PlantPromDB: http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
二、程序
Audic: http://igs-server.cnrs-mrs.fr/~audic/selfid.html
ConPro: http://stl.bioinformatics.med.umich.edu/conpro/
ConSite: http://mordor.cgb.ki.se/cgi-bin/CONSITE/consite/
Dragon Promoter Finder: http://research.i2r.a-star.edu.sg/promoter/promoter1_4/DPF.htm
Eponine: http://servlet.sanger.ac.uk:8080/eponine/
FastM: Now available through Genomatix only
FastM, Patch (PatSearch), Match (MatInspector)....(Transfac 6.0) - programs link:http://www.gene-regulation.de/
FootPrinter: http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput2.pl
McPromoter: http://genes.mit.edu/McPromoter.html
PromFD (download): ftp://ftp.genetics.wustl.edu/pub/stormo/PromFD
PromFind: http://www.rabbithutch.com/
PromFind (download): http://iubio.bio.indiana.edu:7780/perl/custom/index.cgi?dir=/public/molbio/dna/analysis/PromFind
PromoterInspector: http://www.genomatix.de/cgi-bin/promoterinspector/promoterinspector.pl
PromoterScan 2:http://bimas.dcrt.nih.gov:80/molbio/proscan/
Promoter2.0: http://www.cbs.dtu.dk/services/Promoter/
Regulatory Sequence Analysis Tools: http://rsat.ulb.ac.be/rsat/
SignalScan: http://bimas.dcrt.nih.gov:80/molbio/signal/
Tess: http://www.cbil.upenn.edu/tess/
TFSearch: http://www.cbrc.jp/research/db/TFSEARCH.html
TSSG/TSSW/TSSP: http://www.softberry.com/berry.phtml
Arabidopsis, Yeast: http://rulai.cshl.org/software/index1.htm
Pipmaker: http://bio.cse.psu.edu/pipmaker/
Vista:http://www-gsd.lbl.gov/vista/
rVista: http://rvista.dcode.org/
三、在线工具
ConPro: http://stl.bioinformatics.med.umich.edu/conpro/
ConSite: http://mordor.cgb.ki.se/cgi-bin/CONSITE/consite/
Dragon Promoter Finder: http://research.i2r.a-star.edu.sg/promoter/promoter1_4/DPF.htm
Eponine: http://servlet.sanger.ac.uk:8080/eponine/
FastM: Now available through Genomatix only
FastM, Patch (PatSearch), Match (MatInspector)....(Transfac 6.0) - programs link:http://www.gene-regulation.de/
FootPrinter: http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput2.pl
McPromoter: http://genes.mit.edu/McPromoter.html
PromFD (download): ftp://ftp.genetics.wustl.edu/pub/stormo/PromFD
PromFind: http://www.rabbithutch.com/
PromFind (download): http://iubio.bio.indiana.edu:7780/perl/custom/index.cgi?dir=/public/molbio/dna/analysis/PromFind
PromoterInspector: http://www.genomatix.de/cgi-bin/promoterinspector/promoterinspector.pl
PromoterScan 2:http://bimas.dcrt.nih.gov:80/molbio/proscan/
Promoter2.0: http://www.cbs.dtu.dk/services/Promoter/
Regulatory Sequence Analysis Tools: http://rsat.ulb.ac.be/rsat/
SignalScan: http://bimas.dcrt.nih.gov:80/molbio/signal/
Tess: http://www.cbil.upenn.edu/tess/
TFSearch: http://www.cbrc.jp/research/db/TFSEARCH.html
TSSG/TSSW/TSSP: http://www.softberry.com/berry.phtml
Arabidopsis, Yeast: http://rulai.cshl.org/software/index1.htm
Pipmaker: http://bio.cse.psu.edu/pipmaker/
Vista:http://www-gsd.lbl.gov/vista/
rVista: http://rvista.dcode.org/
三、在线工具
http://www.bioinf.man.ac.uk/%7Elockwood/bindgene.html
http://bioprospector.stanford.edu/
http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp
http://melina.hgc.jp/
http://www.bioinfo.tsinghua.edu.cn/%7Ezhengjsh/OTFBS/
http://www.lsi.upc.es/~alggen/recerca/promo_v2/frame-promo.html
http://bimas.dcrt.nih.gov/molbio/signal/
http://www.cbil.upenn.edu/tess/
http://www.ifti.org/
http://bioprospector.stanford.edu/
http://siriusb.umdnj.edu:18080/EZRetrieve/index.jsp
http://melina.hgc.jp/
http://www.bioinfo.tsinghua.edu.cn/%7Ezhengjsh/OTFBS/
http://www.lsi.upc.es/~alggen/recerca/promo_v2/frame-promo.html
http://bimas.dcrt.nih.gov/molbio/signal/
http://www.cbil.upenn.edu/tess/
http://www.ifti.org/
很多是针对特定特种的，如EPD主要针对真核生物，USCS主要针对哺乳动物如人、老鼠、猫、狗等，所以寻找启动子时应根据物种不同选择合适的工具。
https://blog.sciencenet.cn/blog-247480-483245.html
上一篇：mRNA序列、cDNA序列、ORF序列、CDS序列、Promoter、STS、ETS
下一篇：唐僧西天取经每天走了多少步
