RAPSearch: a fast protein similarity search tool for short reads.
RAPSearch: a fast protein similarity search tool for short reads.
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DOI：
10.1186/1471-2105-12-159
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发表时间：
2011-05-15
影响因子：
3
通讯作者：
Tang H
中科院分区：
文献类型：
--
作者：
Ye Y;Choi JH;Tang H
下一代测序（NGS）正在产生大量的短DNA片段，影响着宏基因组学等新兴领域。蛋白质相似性搜索--在这些短读段中实现蛋白质编码基因注释并鉴定其生物学功能的关键步骤--由于短读段数据集的大小而面临着艰巨的挑战。我们开发了一个快速的蛋白质相似性搜索工具RAPSearch，利用减少的氨基酸字母表和后缀数组来检测灵活长度的种子。对于我们测试的短读段（翻译为6帧），与BLASTX相比，RAPSearch实现了约20-90倍的加速。RAPSearch仅遗漏了一小部分（~1.3-3.2%）BLASTX相似性命中，但它也发现了BLASTX遗漏的其他同源蛋白（~0.3-2.1%）。相比之下，BLAT，一种甚至比RAPSearch稍快的工具，与RAPSearch和BLAST相比，灵敏度显著降低。RAPSearch作为开源软件实施，可在http://omics.informatics.indiana.edu/mg/RAPSearch上访问。它可以更快地进行蛋白质相似性搜索。还展示了RAPSearch在元年龄组学中的应用。
Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.
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DOI：
10.1093/protein/13.3.149
发表时间：
2000-03-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Murphy, LR;Wallqvist, A;Levy, RM
通讯作者：
Levy, RM
影响因子：
5.8
作者：
Li, WZ;Jaroszewski, L;Godzik, A
通讯作者：
Godzik, A
DOI：
10.1126/science.1183605
发表时间：
2010-05-21
期刊：
Science (New York, N.Y.)
影响因子：
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作者：
Human Microbiome Jumpstart Reference Strains Consortium;Nelson KE;Weinstock GM;Highlander SK;Worley KC;Creasy HH;Wortman JR;Rusch DB;Mitreva M;Sodergren E;Chinwalla AT;Feldgarden M;Gevers D;Haas BJ;Madupu R;Ward DV;Birren BW;Gibbs RA;Methe B;Petrosino JF;Strausberg RL;Sutton GG;White OR;Wilson RK;Durkin S;Giglio MG;Gujja S;Howarth C;Kodira CD;Kyrpides N;Mehta T;Muzny DM;Pearson M;Pepin K;Pati A;Qin X;Yandava C;Zeng Q;Zhang L;Berlin AM;Chen L;Hepburn TA;Johnson J;McCorrison J;Miller J;Minx P;Nusbaum C;Russ C;Sykes SM;Tomlinson CM;Young S;Warren WC;Badger J;Crabtree J;Markowitz VM;Orvis J;Cree A;Ferriera S;Fulton LL;Fulton RS;Gillis M;Hemphill LD;Joshi V;Kovar C;Torralba M;Wetterstrand KA;Abouellleil A;Wollam AM;Buhay CJ;Ding Y;Dugan S;FitzGerald MG;Holder M;Hostetler J;Clifton SW;Allen-Vercoe E;Earl AM;Farmer CN;Liolios K;Surette MG;Xu Q;Pohl C;Wilczek-Boney K;Zhu D
通讯作者：
Zhu D
DOI：
10.1073/pnas.90.12.5873
发表时间：
1993-06-15
影响因子：
11.1
作者：
KARLIN, S;ALTSCHUL, SF
通讯作者：
ALTSCHUL, SF
影响因子：
3
作者：
Meyer, F.;Paarmann, D.;Edwards, R. A.
通讯作者：
Edwards, R. A.