【分享】基因启动子分析网址和软件

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/