NGSmethDB is a dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.

Just now, the database is being updated. Major novelties include:

  1. Higher-quality maps. In addition to the stringent quality controls included in the previous versions of the NGSmethDB, we now include indels detection and automatic M-bias trimming. This will potentially reduce biases not considered before for the estimation of methylation levels.
  2. Differential methylation. Given the increasing biological relevance of differential methylation, a section of the database is now dedicated to precompiled differentially methylated cytosines (DMCs).
  3. Improved data access. A RESTful API now serve numeric methylome data, allowing the selection by species, assembly, chromosome and genome region. Data for a pair of tissues can be simultaneously retrieved in table format, thus enabling the comparison of differential methylation among different tissues or different physiological/pathological conditions. Furthermore, the on-line connection through other public APIs allows to retrieve updated third-part annotations on any DMC in the database.
  4. Data sharing and visualization. The browser implemented in previous versions is now replaced by standard track hubs. In this way, NGSmethDB data can be now visualized and compared to a plethora of third-part annotations by means of the powerful UCSC or ENSEMBL Genome Browsers. In addition, tools as the Table Browser provides an easy way to 1) retrieve to the local machine detailed NGSmethDB datasets from any genome, chromosome, genome region, gene, SNP or whatever other genome marker; 2) combine methylation data and any other third-part annotation into a single set of data based on specific join criteria –for example, this can be used to find the methylation state of cytosines that intersect with CpG islands; and 3) directly upload NGSmethDB datasets to public bioinformatic platforms as Galaxy, GenomeSpace or GREAT for further downstream analyses.
  5. Confidentiality issues. The RESTful API will be made available soon for download. In this way, the user will no longer need to upload private data to the server to carry out comparative analyses against NGSmethDB data.

How to cite

[1] Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg and José L. Oliver. 2014. NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. Nucl. Acids Res. (1 January 2014) 42 (D1): D53-D59 first published online November 22, 2013 doi:10.1093/nar/gkt1202
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[2] Michael Hackenberg, Guillermo Barturen and José L. Oliver. 2010. NGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data
Nucleic Acids Research, 2010, 1–5 [PDF]