生物分析常用工具及网站

生物分析常用工具及网站

Resource	Purpose	URL
Batman	MeDIP DNA methylation analysis tool	http://td-blade.gurdon.cam.ac.uk/software/batman
BDPC	DNA methylation analysis platform	http://biochem.jacobs-university.de/BDPC
BSMAP	Whole-genome bisulphite sequence mapping	http://code.google.com/p/bsmap
CpG Analyzer	Windows-based program for bisulphite DNA	-
CpGcluster	CpG island identification	http://bioinfo2.ugr.es/CpGcluster
CpGFinder	Online program for CpG island identification	http://linux1.softberry.com
CpG Island Explorer	Online program for CpG Island identification	http://bioinfo.hku.hk/cpgieintro.html
CpG Island Searcher	Online program for CpG Island identification	http://cpgislands.usc.edu
CpG PatternFinder	Windows-based program for bisulphite DNA	-
CpG Promoter	Large-scale promoter mapping using CpG islands	http://www.cshl.edu/OTT/html/cpg_promoter.html
CpG ratio and GC content Plotter	Online program for plotting the observed:expected ratio of CpG	http://mwsross.bms.ed.ac.uk/public/cgi-bin/cpg.pl
CpGviewer	Bisulphite DNA sequencing viewer	http://dna.leeds.ac.uk/cpgviewer
CyMATE	Bisulphite-based analysis of plant genomic DNA	http://www.gmi.oeaw.ac.at/en/cymate-index/
EMBOSS	CpGPlot/CpGReport/Isochore Online program for plotting CpG-rich regions	http://www.ebi.ac.uk/Tools/emboss/cpgplot/index.html
Epigenomics Roadmap	NIH Epigenomics Roadmap Initiative homepage	http://nihroadmap.nih.gov/epigenomics
Epinexus	DNA methylation analysis tools	http://epinexus.net/home.html
MEDME	Software package (using R) for modelling MeDIP experimental data	http://espresso.med.yale.edu/medme
methBLAST	Similarity search program for bisulphite-modified DNA	http://medgen.ugent.be/methBLAST
MethDB	Database for DNA methylation data	http://www.methdb.de
MethPrimer	Primer design for bisulphite PCR	http://www.urogene.org/methprimer
methPrimerDB	PCR primers for DNA methylation analysis	http://medgen.ugent.be/methprimerdb
MethTools	Bisulphite sequence data analysis tool	http://www.methdb.de
MethyCancer Database	Database of cancer DNA methylation data	http://methycancer.psych.ac.cn
Methyl Primer Express	Primer design for bisulphite PCR	http://www.appliedbiosystems.com/methylprimerexpress
Methylumi	Bioconductor package for analysing DNA methylation data from Illumina platforms	http://www.bioconductor.org/packages/bioc/html/methylumi.html
Methylyzer	Bisulphite DNA sequence visualization tool	http://ubio.bioinfo.cnio.es/Methylyzer/main/index.html
mPod	Genome-wide DNA methylation viewer integrated with the Ensembl genome browser	http://www.compbio.group.cam.ac.uk/Projects/p4meth.html
PubMeth	Database of DNA methylation literature	http://www.pubmeth.org
QUMA	Quantification tool for methylation analysis	http://quma.cdb.riken.jp
TCGA Data Portal	Database of TCGA DNA methylation data	http://cancergenome.nih.gov/dataportal