NGSmethDB: Database for next-generation sequencing whole genome methylation

Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution. This allows studying the absence of methylation in a particular genome region over a range of tissues, the differential tissue methylation or the changes occurring along pathological conditions. The first database NGSmethDB proposed by Spanish scientists fully address such requirements for the storage and retrieval of methylation data derived from NGS (published in Molecular biology and Evolution) . The database uses a web interface based on GBrowse and coupled to a MySQL backend, which allows to visualize the methylation data in a genomic context together with many other annotations, as well as full data downloads.

Basic features of the database:

1. Two different cytosine methylation contexts are considered. First, the CpG dinucleotides and second the CAG/CTG pattern, which have been shown recently to be able to methylate in undifferentiated cells.
2. The user can search for all methylation contexts which are unmethylated or differentially methylated in a given set of tissues.
3. The user can retrieve all methylation values for a given set of tissues in a given chromosomal region.
4. The database allows displaying the methylation among different tissues in the promoter regions of RefSeq genes.
5. Methylation values can be retrieved for a given chromosomal region.
6. Dump downloads exist for two different read coverage: methylation contexts covered by at least 1 read, and those covered by at least 10 reads.

NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research.