Some websites for DNA methylation and chromatin

epigenetics databases and tools

UCSC Genome Browser with ENCODE and other data tracks: http://genome.ucsc.edu/

Includes DNA methylation, CpG island, histone modification, CTCF binding, RNA-seq, CAGE
tagging, predicted chromatin structures (Chromatin state segmentation by HMM), DNaseI
hypersensitivity mapping for human cell cultures and tissues with some of these tracks for the
mouse

In addition: Track Data Hubs at https://genome.ucsc.edu/cgi-bin/hgHubConnect

http://smithlabresearch.org/software/methbase/

Online training for UCSC Genome Browser: https://www.genome.ucsc.edu/training/

ROADMAP Epigenomics Project: http://epigenomebrowser.org

ROADMAP tutorial: http://www.nature.com/nbt/journal/vaop/ncurrent/extref/nbt.3158-S2.pdf

Galaxy for computational biology: http://galaxyproject.org/

Human Epigenome Atlas: http://www.genboree.org/epigenomeatlas/multiGridViewerPublic.rhtml

MethylomeDB, The Brain Methylome Database: http://www.neuroepigenomics.org/methylomedb/

MethDB: data base for DNA methylation and environmental epigenetic effects: http://www.methdb.de/

Cancer Methylome System: http://cbbiweb.uthscsa.edu/KMethylomes/tmv_info.jsp

DiseaseMeth: A web based resource focused on the aberrant methylomes of human diseases:
http://202.97.205.78/diseasemeth/

Primer design for bisulfite-treated DNA,
UroGene: http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi

BiSearch: http://bisearch.enzim.hu/

MethPrimer for CpG island prediction too: http://bisearch.enzim.hu/2

Bisulfite Primer Seeker: http://www.zymoresearch.com/tools/bisulfite-primer-seeker

Bismark, mapping bisulfite-converted DNA sequence reads:http://www.bioinformatics.babraham.ac.uk/projects/bismark/

methylkit, annotation of RRBS profiles: https://code.google.com/p/methylkit/

Histone modification database: http://www.actrec.gov.in/histome/index.php

Human histone modification database: http://202.97.205.78/hhmd/Search.jsp