Format

Send to

Choose Destination
Nucleic Acids Res. 2014 Jan;42(Database issue):D53-9. doi: 10.1093/nar/gkt1202. Epub 2013 Nov 22.

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.

Author information

1
Facultad de Ciencias, Departmento de Genética, Universidad de Granada, 18071-Granada, Spain and Laboratorio de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, 18100-Granada, Spain.

Abstract

The updated release of 'NGSmethDB' (http://bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. Short-read data sets from NGS bisulfite-sequencing projects of cell lines, fresh and pathological tissues are first pre-processed and aligned to the corresponding reference genome, and then the cytosine methylation levels are profiled. One major improvement is the application of a unique bioinformatics protocol to all data sets, thereby assuring the comparability of all values with each other. We implemented stringent quality controls to minimize important error sources, such as sequencing errors, bisulfite failures, clonal reads or single nucleotide variants (SNVs). This leads to reliable and high-quality methylomes, all obtained under uniform settings. Another significant improvement is the detection in parallel of SNVs, which might be crucial for many downstream analyses (e.g. SNVs and differential-methylation relationships). A next-generation methylation browser allows fast and smooth scrolling and zooming, thus speeding data download/upload, at the same time requiring fewer server resources. Several data mining tools allow the comparison/retrieval of methylation levels in different tissues or genome regions. NGSmethDB methylomes are also available as native tracks through a UCSC hub, which allows comparison with a wide range of third-party annotations, in particular phenotype or disease annotations.

PMID:
24271385
PMCID:
PMC3964946
DOI:
10.1093/nar/gkt1202
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center