Software/Computational epigenetics

• Introduction:
  • Computational epigenetics in Wikipedia.

• for finding the region of interest:
  • CpG island Searcher (D.Takai) screens DNA sequences for CpG islands and generates a graphical output.
• for prediction of methylation probability:
  • Methylator attempts to predict whether CpG in a DNA sequence are likely to be methylated or not.
• for primer design and verification:
  • MethPrimer (Long-Cheng Li) is a on-line tool for designing bisulfite-conversion-based Methylation PCR Primers. It can design primers for Methylation-Specific PCR (MSP) and Bisulfite-Sequencing PCR or Bisulfite-Restriction PCR. The input sequence is DNA sequence in any format. The program returns results in both text and graphic view.
  • BiSearch provides access to a PCR primer-test and primer-design algorithm that can used for both bisulfite converted and not modified sequences. You can search various genomes with the designed primers by a fast ePCR method.
  • Microsoft Word Macro for Analysis of Cytosine Methylation made by Rakesh Singal, M.D. This macro (i) converts genomic sequence to modified sequence that would result after bisulfite treatment facilitating primer design for bisulfite genomic sequencing and methylation-sensitive PCR assay and (ii) identifies restriction sites that are preserved in bisulfite-converted and PCR-amplified product only if cytosine residues at relevant CpG dinucleotides are methylated (and thereby not converted to uracil) in the genomic DNA.
  • methBLAST (Jo Vandesompele) allows you to check your primers for bisulfite converted DNA by blasting them against the unmethylated and methylated genomic sequences of man, mouse and rat. Work is in progress.
• for COmbined Bisulfite Restriction Assay
  • snake-charmer - a tool for the selection of restriction enzymes for COBRA
• for analysis of bisulfite sequencing data:
  • MethTools 1.x and MethTools 2.x - collection of software tools for the analysis of bisulfite treated DNA. The software does the comparison between unconverted mother sequences and deaminated sequences, generates graphical outputs of methylation patterns and methylation density, estimates the systematic error of the experiment and searches for conserved methylated nucleotide-patterns. The software can be used to generate files suitable for the submission to MethDB.
  • BiQ Analyzer (Christoph Bock) - this excellent java tool facilitates the data analysis considerably. A must for each bisulfiter. Generates archive files that can directly be uploaded to MethDB.
  • CpGviewer (Ian Carr) - a Windows program for the interactive editing of the bisulfite derived sequences that are aligned to a reference sequence.
  • CyMATE - analysis of bisulfite sequencing. Results are send back by email.
  • BISMA - Bisulfite Sequencing DNA Methylation Analysis at the University of Bremen
• for integration of your data into the distributed annotation system (DAS)
  • eL-DASionator - an LDAS upload file generator

Related databases

• REBASE - the Restriction enzyme database
• The imprinted gene and parent-of-origin effect database
• List of Promoter CpG Island Hypermethylation in Cancer (broken link)
• Rett Syndrome database
• MECP2 variation database
• methPrimerDB - a database of primer sequences used in PCR based methylation methods
• CREMOFAC - a database of amino acid sequences of chromatin remodeling factors
• PubMeth - a database of DNA methylation in cancer based on automated textmining of Medline/PubMed abstracts. The database is manually curated and annotated
• MethCancer DB - a database of abberrant CpG methylation in human tumours
• MethyCancer is part of the Cancer Epigenomics Project in China
• NCBI Epigenomics Sample Browser provides access to a large number of epigenetic data sets.
• Antibody Validation Database - antibodies for Western blot and ChIP validated by independent labs.

Related sites

• Arabidopsis thaliana
  • Genome browser of the The SIGnAL Arabidopsis Methylome Mapping Tool
  • Project page of the microarray based methylation analysis of the Arabidopsis thaliana genome with links to genome browser and data download
  • Shotgun Bisulphite Sequencing of the Arabidopsis Genome
• Human
  • Human Epigenome Project
  • German National Methylome project for human chromosome 21 (NAME 21)
  • Results of bisulfite sequencing of CGI on chromosome 21 (NAME 21)
  • Methylation Landscape of the Human Genome at the Columbia University (broken link)
  • The Human DNA Methylome at the Salk Institute
• Next generation sequencing raw data
  • Sequence Read Archive at the NCBI
• NGSmethDB - a database for next-generation sequencing single-cytosine-resolution DNA methylation data
• DNA Methylation Society (DMS)
• DNA Methylation in Cancer at the M. D. Anderson Cancer Center
• CpG Island Tagging Project at the Sanger Institute