Fast computation and applications of genome mappability

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  • dc.contributor.author Derrien, Thomasca
  • dc.contributor.author Estellé, Jordica
  • dc.contributor.author Marco Sola, Santiagoca
  • dc.contributor.author Knowles, David G.ca
  • dc.contributor.author Raineri, Emanueleca
  • dc.contributor.author Guigó Serra, Rodericca
  • dc.contributor.author Ribeca, Paoloca
  • dc.date.accessioned 2014-06-20T08:18:15Z
  • dc.date.available 2014-06-20T08:18:15Z
  • dc.date.issued 2012ca
  • 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/pdfca
  • 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.0030377ca
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0030377
  • dc.identifier.issn 1932-6203ca
  • dc.identifier.uri http://hdl.handle.net/10230/22592
  • dc.language.iso engca
  • dc.publisher Public Library of Science (PLoS)ca
  • dc.relation.ispartof PLoS One. 2012;7(1):e30377
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2006-03380
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
  • dc.rights © 2012 Thomas Derrien et al. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licenseca
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • 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 mappabilityca
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

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