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        【分享】基因启动子分析网址和软件

        丁香园论坛

        6371
        Promoter Searching - Lecture Links

        Lecture 1: From mRNA to Genomic Sequence - Defining the Genomic Region
        • RefSeq: http://www.ncbi.nlm.nih.gov/RefSeq/
        • NEDO: http://www.kazusa.or.jp/NEDO/
        • NEDO home: http://www.nedo.go.jp/bio-e/index.html
        • Kasuza home: http://www.kazusa.or.jp/en/human/
        • HUGE (Kasuza): http://www.kazusa.or.jp/huge/
        • RIKEN: http://genome.gsc.riken.go.jp/
        • Mammalian Gene Collection: http://mgc.nci.nih.gov/
        • FirstEF: http://rulai.cshl.org/tools/FirstEF/

        Lecture 2: States of Common Eukaryotic Genomes
        Multi-Genome viewers
        • NCBI: http://www.ncbi.nlm.nih.gov/mapview/static/MVstart.html
        • UCSC: http://genome.ucsc.edu/
        • Ensembl: http://www.ensembl.org/
        Various Organisms:
        Mouse:
        • NCBI Genome Resources: http://www.ncbi.nlm.nih.gov/genome/guide/mouse/
        • Mouse Genome Informatics: http://www.informatics.jax.org/
        Rat:
        • NCBI Genome Resources: http://www.ncbi.nlm.nih.gov/genome/guide/rat/index.html
        • Baylor Genome Sequencing: http://hgsc.bcm.tmc.edu/projects/rat/
        • Rat Genome Database: http://rgd.mcw.edu/
        Yeast:
        • SGD: http://genome-www.stanford.edu/Saccharomyces/
        • Comprehensive Yeast Genome Database: http://mips.gsf.de/proj/yeast/CYGD/db/index.html
        • S_Pombe: http://genome-www.stanford.edu/Saccharomyces/
        Drosophila:
        • FlyBase: http://flybase.bio.indiana.edu:7081/
        • Berkley Drosophila Genome Project: http://www.fruitfly.org/
        Arabidopsis:
        • TAIR - The arabidopsis resource: http://www.arabidopsis.org/
        Rice:
        • Syngenta/TMRI: http://portal.tmri.org/rice/
        • Chinese Academy of Sciences: http://www.genomics.org.cn:7001/
        • TIGR: http://www.tigr.org/tdb/e2k1/osa1/
        • NCBI: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?chr=rice.inf
        • IRSGP: http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/seqcollab.pl

        Lecture 4: Tools for Promoter Searching
        Databases:
        • TFD: http://www.ifti.org/
        • dbTSS (Human): http://dbtss.hgc.jp/samp_home.html
        • EPD: http://www.epd.isb-sib.ch/
        • TRRD: http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd
        • TransFac: http://transfac.gbf.de/TRANSFAC/
        • PlantCare: http://oberon.rug.ac.be:8080/PlantCARE/index.html
        • PlantProm: http://mendel.cs.rhul.ac.uk/mendel.php
        Programs:
        • Audic: http://igs-server.cnrs-mrs.fr/~audic/selfid.html
        • ConPro: http://stl.bioinformatics.med.umich.edu/conpro/
        • Eponine: http://servlet.sanger.ac.uk:8080/eponine/
        • FastM: http://transfac.gbf.de/cgi-bin/fastm/fastm.pl
        • FastM, PatSearch (Patch), MatInspector....(Transfac 6.0) - programs link:http://www.gene-regulation.de/
        • MatInspector 2.2 (TransFac 4.0 matrices): http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl
        • 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 1.7: http://www.cbs.umn.edu/software/promoterscan.htm
        • PromoterScan 2:http://bimas.dcrt.nih.gov/molbio/proscan/
        • Promoter2.0: http://www.cbs.dtu.dk/services/Promoter/>http://www.cbs.dtu.dk/services/Promoter/</A><LI>Regulatory%20Sequence%20Analysis%20Tools:%20<A%20HREF=
        • SignalScan: http://bimas.dcrt.nih.gov/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
        • Zhang Lab - Promoter tools and databases for Human, Drosophila, C. Elegans, 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://nemo.lbl.gov/rvista/
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