SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.
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DOI：
10.1186/1471-2105-12-134
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发表时间：
2011-05-05
影响因子：
3
通讯作者：
This P
中科院分区：
文献类型：
--
作者：
Dereeper A;Nicolas S;Le Cunff L;Bacilieri R;Doligez A;Peros JP;Ruiz M;This P
高通量重测序、新的基因分型技术和参考基因组的可用性允许对许多植物物种中的单核苷酸多态性（SNP）和插入/缺失事件（indels）进行广泛表征。大规模遗传多样性项目产生的重测序和基因分型数据量迅速增加，需要开发能够有效管理、分析和联合收割机这些遗传数据与基因组结构和外部数据的集成生物信息学工具。在这种情况下，我们开发了SNiPlay，一个灵活的，用户友好的和集成的基于Web的工具，致力于多态性的发现和分析。它集成了：1）一个管道，可通过互联网免费访问，将现有软件与新工具相结合，以检测SNP并计算SNP数据的不同类型的统计指数和图形布局。从标准序列比对、基因分型数据或作为输入的桑格测序轨迹中，SNiPlay检测SNP和插入缺失事件，并输出用于设计Illumina SNP芯片的提交文件。随后，它将序列和基因分型数据发送到一系列负责各种过程的模块中：参考基因组的物理映射，注释（基因组位置，内含子/外显子位置，同义/非同义取代），用户定义组中的SNP频率确定，单倍型重建和网络，连锁不平衡评估和多样性分析（Pi，Watterson's Theta，Tajima's D）。此外，管道允许使用外部数据（如表型，地理来源，分类，分层）来定义组和比较统计指数。2)一个数据库，存储多态性，基因分型数据和公共和私人项目发布的葡萄藤序列。它允许用户使用各种过滤器（如基因组位置，缺失数据，多态性类型，等位基因频率）检索SNP，比较人群之间的SNP模式，并以各种格式导出基因分型数据或序列。我们在葡萄藤遗传项目上的实验表明，SNiPlay允许遗传学家在植物遗传多样性的几个关键研究领域快速获得先进的结果。通过自动化和集成，大量SNP数据的管理和处理对于最终用户来说变得更加容易。目前的发展考虑到了高通量技术的新进展。SNiPlay可从以下网址获得：http://sniplay.cirad.fr/。
High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies. SNiPlay is available at: http://sniplay.cirad.fr/.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
7
作者：
Chen, Ken;McLellan, Michael D.;Mardis, Elaine R.
通讯作者：
Mardis, Elaine R.
DOI：
10.1007/s11032-009-9377-5
发表时间：
2010-06
期刊：
Molecular breeding : new strategies in plant improvement
影响因子：
--
作者：
Anithakumari AM;Tang J;van Eck HJ;Visser RG;Leunissen JA;Vosman B;van der Linden CG
通讯作者：
van der Linden CG