生物分析常用工具及网站

雨点打透心脏的1/2处 2022-03-31 07:38 448阅读 0赞

## 生物分析常用工具及网站 ##

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