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NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

热1 tlexander 添加于 2010-11-15 00:19 | 3023 次阅读 | 0 个评论

作者
Hackenberg M, Barturen G, Oliver JL
摘要
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.
详细资料
- 文献种类:期刊
- 期刊名称: Nucleic Acids Research
- 期刊缩写: Nucleic Acids Res
- 期卷页: 2010年
- 地址: Dpto. de Genetica, Facultad de Ciencias, Universidad de Granada, 18071-Granada and Lab. de Bioinformatica, Inst. de Biotecnologia, Centro de Investigacion Biomedica, 18100-Granada, Spain
- ISBN: 0305-1048
- 备注:PMID:20965971
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