SeqAnt: a web service to rapidly identify and annotate DNA sequence variations.
SeqAnt: a web service to rapidly identify and annotate DNA sequence variations.
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DOI：
10.1186/1471-2105-11-471
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发表时间：
2010-09-20
影响因子：
3
通讯作者：
Zwick ME
中科院分区：
文献类型：
--
作者：
Shetty AC;Athri P;Mondal K;Horner VL;Steinberg KM;Patel V;Caspary T;Cutler DJ;Zwick ME
第二代测序平台的巨大通量和低成本现在允许研究和临床遗传学家常规地进行单个实验，识别数万到数百万个变异位点。现有的方法是通过网络浏览器使用来自公共数据库的信息来标注变异位点，这种方法太慢，无法用于遗传学家常规生成的大型测序数据集。由于变异位点的序列注释需要在功能表征之前进行，因此缺乏高通量的管道来有效地注释变异位点可能成为遗传学研究的重大瓶颈。SeqAnt （Sequence Annotator）是一个开源的web服务和软件包，可以快速注释DNA序列变体，并识别人类、小鼠、苍蝇和蠕虫基因组测序实验中的隐性或复合杂合位点。变异的特征在于它们的功能类型、频率和进化守恒。带注释的变体可以在web浏览器上查看，以标签分隔的文本文件下载，或直接以BED格式上传到UCSC基因组浏览器。为了证明SeqAnt的速度，我们对一系列公开可用的数据集进行了注释，这些数据集的大小从37到3,439,107个变异位点不等。完全注释这些数据的总时间从0.17秒到28分49.8秒不等。SeqAnt是一个开源的网络服务和软件包，它克服了研究和临床遗传学家使用第二代测序平台面临的关键瓶颈。SeqAnt将被证明对那些在实验室中缺乏专门的生物信息学人员或基础设施的研究人员特别有用。
The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. SeqAnt (Sequence Annotator) is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
5.8
作者：
Johnson, Andrew D.;Handsaker, Robert E.;de Bakker, Paul I. W.
通讯作者：
de Bakker, Paul I. W.
影响因子：
7
作者：
Pollard, Katherine S.;Hubisz, Melissa J.;Siepel, Adam
通讯作者：
Siepel, Adam
影响因子：
5.8
作者：
Gamazon, Eric R.;Zhang, Wei;Cox, Nancy J.
通讯作者：
Cox, Nancy J.
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