BiQ Analyzer - a software tool for DNA methylation analysis

Resources for DNA Methylation Research

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

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

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 References on how to cite BiQ Analyzer