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dc.contributor.authorGeisen, Stefanie
dc.contributor.authorBarturen, Guillermo
dc.contributor.authorAlganza, Ángel M.
dc.contributor.authorHackenberg , Michael 
dc.contributor.authorOliver, José Luis
dc.date.accessioned2014-10-07T08:23:16Z
dc.date.available2014-10-07T08:23:16Z
dc.date.issued2014
dc.identifier.citationGeisen, S.; et al. NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. Nucleic Acids Research, 42(1): 53-59 (2014). [http://hdl.handle.net/10481/33365]es_ES
dc.identifier.issn1362-4962
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/10481/33365
dc.description.abstractThe 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.es_ES
dc.description.sponsorshipSpanish Government [BIO2008-01353 to J.L.O. and BIO2010-20219 to M.H.], and Basque country ‘AE’ grant (to G.B.). Funding for open access charge: Department of Genetics, University of Granada, Spain.es_ES
dc.language.isoenges_ES
dc.publisherOxford University Presses_ES
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivs 3.0 Licensees_ES
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/es_ES
dc.subjectNGSmethDBes_ES
dc.subjectGenomees_ES
dc.subjectSingle-cytosine resolution methylomeses_ES
dc.titleNGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomeses_ES
dc.typeinfo:eu-repo/semantics/articlees_ES
dc.rights.accessRightsinfo:eu-repo/semantics/openAccesses_ES
dc.identifier.doi10.1093/nar/gkt1202


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