Fast computation and applications of genome mappability.

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 m...

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Autores principales:	Thomas Derrien, Jordi Estellé, Santiago Marco Sola, David G Knowles, Emanuele Raineri, Roderic Guigó, Paolo Ribeca
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5bfaabaf5be54ea0877d847ee3c5f7d5
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spelling	oai:doaj.org-article:5bfaabaf5be54ea0877d847ee3c5f7d52021-11-18T07:29:48ZFast computation and applications of genome mappability.1932-620310.1371/journal.pone.0030377https://doaj.org/article/5bfaabaf5be54ea0877d847ee3c5f7d52012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22276185/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203We 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).Thomas DerrienJordi EstelléSantiago Marco SolaDavid G KnowlesEmanuele RaineriRoderic GuigóPaolo RibecaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e30377 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Thomas Derrien Jordi Estellé Santiago Marco Sola David G Knowles Emanuele Raineri Roderic Guigó Paolo Ribeca Fast computation and applications of genome mappability.
description	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).
format	article
author	Thomas Derrien Jordi Estellé Santiago Marco Sola David G Knowles Emanuele Raineri Roderic Guigó Paolo Ribeca
author_facet	Thomas Derrien Jordi Estellé Santiago Marco Sola David G Knowles Emanuele Raineri Roderic Guigó Paolo Ribeca
author_sort	Thomas Derrien
title	Fast computation and applications of genome mappability.
title_short	Fast computation and applications of genome mappability.
title_full	Fast computation and applications of genome mappability.
title_fullStr	Fast computation and applications of genome mappability.
title_full_unstemmed	Fast computation and applications of genome mappability.
title_sort	fast computation and applications of genome mappability.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/5bfaabaf5be54ea0877d847ee3c5f7d5
work_keys_str_mv	AT thomasderrien fastcomputationandapplicationsofgenomemappability AT jordiestelle fastcomputationandapplicationsofgenomemappability AT santiagomarcosola fastcomputationandapplicationsofgenomemappability AT davidgknowles fastcomputationandapplicationsofgenomemappability AT emanueleraineri fastcomputationandapplicationsofgenomemappability AT rodericguigo fastcomputationandapplicationsofgenomemappability AT paoloribeca fastcomputationandapplicationsofgenomemappability
_version_	1718423345983127552

Fast computation and applications of genome mappability.

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