Fast computation and applications of genome mappability.
Fast computation and applications of genome mappability.
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DOI：
10.1371/journal.pone.0030377
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Ribeca P
中科院分区：
文献类型：
--
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
我们提出了一个快速映射为基础的算法来计算一个参考基因组的每个区域的可映射到指定数量的错配。了解基因组的可映射性对于解释大规模并行测序实验至关重要。我们研究真核生物DNA/RNA的可映射性作为一个整体，并在基因家族的水平，提供各种生物体的轨道，使可映射性信息进行可视化探索的属性。此外，我们表明，映射能力物种和基因类之间的差异很大。最后，我们提出了几个实际应用，其中可映射性可用于完善高通量测序数据的分析（SNP调用，基因表达定量和配对末端实验）。这项工作突出了映射性作为一个重要的概念，值得充分考虑，特别是当大规模并行测序技术。GEM可映射性程序属于GEM（GEnome Multitool）程序套件，可从其网站（http：//www.example.com）免费下载以供任何用途。gemlibrary.sourceforge.net
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).
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影响因子：
56.9
作者：
Bailey, JA;Gu, ZP;Eichler, EE
通讯作者：
Eichler, EE
DOI：
10.1093/bioinformatics/btp692
发表时间：
2010-02-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li B;Ruotti V;Stewart RM;Thomson JA;Dewey CN
通讯作者：
Dewey CN
UCSC基因组浏览器数据库：更新2010。
影响因子：
14.9
作者：
Rhead B;Karolchik D;Kuhn RM;Hinrichs AS;Zweig AS;Fujita PA;Diekhans M;Smith KE;Rosenbloom KR;Raney BJ;Pohl A;Pheasant M;Meyer LR;Learned K;Hsu F;Hillman-Jackson J;Harte RA;Giardine B;Dreszer TR;Clawson H;Barber GP;Haussler D;Kent WJ
通讯作者：
Kent WJ
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
48
作者：
Mortazavi, Ali;Williams, Brian A.;Wold, Barbara
通讯作者：
Wold, Barbara