Welcome to the UPF Digital Repository

Fast computation and applications of genome mappability

Show simple item record

dc.contributor.author Derrien, Thomas
dc.contributor.author Estellé, Jordi
dc.contributor.author Marco Sola, Santiago
dc.contributor.author Knowles, David G.
dc.contributor.author Raineri, Emanuele
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Ribeca, Paolo
dc.date.accessioned 2014-06-20T08:18:15Z
dc.date.available 2014-06-20T08:18:15Z
dc.date.issued 2012
dc.identifier.citation Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R et al./nFast computation and applications of genome mappability. PLoS One. 2012; 7(1): e30377. DOI: 10.1371/journal.pone.0030377
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10230/22592
dc.description.abstract We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of massively parallel sequencing experiments. We investigate the properties of the mappability of eukaryotic DNA/RNA both as a whole and at the level of the gene family, providing for various organisms tracks which allow the mappability information to be visually explored. In addition, we show that mappability varies greatly between species and gene classes. Finally, we suggest several practical applications where mappability can be used to refine the analysis of high-throughput sequencing data (SNP calling, gene expression quantification and paired-end experiments). This work highlights mappability as an important concept which deserves to be taken into full account, in particular when massively parallel sequencing technologies are employed. The GEM mappability program belongs to the GEM (GEnome Multitool) suite of programs, which can be freely downloaded for any use from its website (http://gemlibrary.sourceforge.net).
dc.description.sponsorship This work has been partially supported by grants BIO2006-03380 (to RG) and CONSOLIDER CSD2007-00050 (to RG and PR) from the Spanish Ministerio de Educacion y Ciencia
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.rights © 2012 Thomas Derrien et al. This is an Open Access article distributed under the terms of a Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by/2.5/
dc.subject.other Algorismes
dc.subject.other Biologia computacional -- Mètodes
dc.subject.other Genoma humà
dc.subject.other Seqüència de nucleòtids
dc.title Fast computation and applications of genome mappability
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0030377
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2006-03380
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


This item appears in the following Collection(s)

Show simple item record

Search DSpace


Advanced Search

Browse

My Account

Statistics

Compliant to Partaking