2026-04-17T17:08:54Zhttps://recercat.cat/oai/requestoai:recercat.cat:10230/225922025-12-12T03:42:38Zcom_2072_6col_2072_452952
RECERCAT
author
Derrien, Thomas
author
Estellé, Jordi
author
Marco Sola, Santiago
author
Knowles, David G.
author
Raineri, Emanuele
author
Guigó Serra, Roderic
author
Ribeca, Paolo
2014-06-20T08:18:15Z2014-06-20T08:18:15Z2012
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).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
© 2012 Thomas Derrien et al. This is an Open Access article distributed under the terms of a Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/ info:eu-repo/semantics/openAccess
Algorismes
Biologia computacional -- Mètodes
Genoma humà
Seqüència de nucleòtids
Fast computation and applications of genome mappability
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion