Open AccessNGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
Author(s) -
Michael Hackenberg,
Guillermo Barturen,
José Luis Tejera Oliver
Publication year - 2010
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkq942
Subject(s) - biology , dna methylation , methylation , cpg site , illumina methylation assay , computational biology , genome , genome browser , genetics , bisulfite sequencing , genomics , database , gene , computer science , gene expression
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. However, no database exists fully addressing such requirements. We propose here NGSmethDB (http://bioinfo2.ugr.es/NGSmethDB/gbrowse/) for the storage and retrieval of methylation data derived from NGS. Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface coupled to a MySQL backend and several data mining tools, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. NGSmethDB is currently populated with human, mouse and Arabidopsis data, but other methylomes will be incorporated through an automatic pipeline as soon as new data become available. Dump downloads for three coverage levels (1, 5 or 10 reads) are available. NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research.