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BiQ Analyzer - a software tool for DNA methylation analysis
Resources for DNA Methylation Research
Preparing experimental analysis :
CpG Island Searcher (
http://cpgislands.usc.edu/
) - identify CpG islands of interest
Protocol Online (
http://www.protocol-online.org/prot/Molecular_Biology/DNA/Methylation_analysis/
) - find appropriate protocols for methylation analysis
MethPrimer (
http://www.urogene.org/methprimer/
) - design primers for MSP, bisulfite sequencing, and restriction enzyme PCR
methBLAST (
http://medgen.ugent.be/methBLAST/
) - BLAST-search bisulfite-converted sequences or primers against the genomes of human, mouse or rat
Analyzing experimental data :
BiQ Analyzer (
http://biq-analyzer.bioinf.mpi-inf.mpg.de/
) - quality control, statistical analysis, and diagram generation for bisulfite sequencing
MethTools (
http://genome.imb-jena.de/methtools/
) - generation of methylation logo plots and some other diagram types
Related databases
MethDB (
http://www.methdb.net/
) - first public database of DNA methylation data
REBASE (
http://rebase.neb.com/rebase/rebase.html
) - restriction enzyme database
Human Epigenome Project (
http://www.sanger.ac.uk/PostGenomics/epigenome/
) - dedicated database for data generated within the HEP
methPrimerDB (
http://medgen.ugent.be/methprimerdb/
) - database of validated methylation-specific primers
Please see
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