51黑料吃瓜在线观看,51黑料官网|51黑料捷克街头搭讪_51黑料入口最新视频

設為首頁 |  加入收藏
首頁首頁 期刊簡介 消息通知 編委會 電子期刊 投稿須知 廣告合作 聯系我們
微生物分類單元聚類算法比較研究

Comparison of the clustering algorithms based on operational taxonomic units

作者: 周晨  張紹武  陳偉 
單位:                      西北工業(yè)大學自動化學院(西安710072)        
關鍵詞:                     聚類;操作分類單元;16S  rRNA基因;微生物          
分類號:
出版年·卷·期(頁碼):2014·33·6(591-597)
摘要:

           目的  隨著高通量測序技術的發(fā)展,產生了大量的微生物16S rRNA基因序列數據。對該數據進行精確的微生物操作分類單元(operational taxonomic unit, OTU)劃分,有助于了解環(huán)境中微生物的種群組成及分布。 方法  本文在真實數據集與模擬數據集上,對現有的7種流行OTU單元聚類算法進行了對比研究,并分析了這些算法的優(yōu)缺點及使用范圍。 結果  序列長度、測序深度對聚類結果均有影響。 結論  相同的序列相似性閾值下,不同的聚類算法聚類結果差異較大,其中CROP算法的魯棒性和抗噪性較好。    

       Objective Recent advance of high-throughput next-generation sequencing technology allows us to generate a great deal of 16S rRNA sequences. We can explore the population composition and distribution of the environmental microbes by accurately clustering the 16S rRNA sequences into operational taxonomic units (OTU). Methods In the present work, we conducted a comprehensive evaluation of seven existing methods for OTU inference based on both real and simulated data, and identified the advantages and limitation of these algorithms. Results We found the sequence length and sequencing depth affected the OTU results. Conclusions At the same sequence similarity threshold, the clustering results of these clustering algorithms are different and the CROP algorithm is robust and insensitive to noise.

參考文獻:

           [1]Karl DM. Microbial oceanography: paradigms, processes and promise[J]. Nature, 2007, 5: 759-767. [2]Pace NR. A molecular view of microbial diversity and the biosphere[J]. Science, 1997, 276(5313):734-740. [3]Sharpton TJ, Riesenfeld SJ, Kembel SW, et al. PhylOTU: A High-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data[J]. PLOS Computational Biology, 2011, 7(1):e1001061. [4]Pruesse E, Quast C, Knittel K, et al. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB[J]. Nucleic Acids Res, 2007, 35:7188-7196. [5]Huse SM, Dethlefsen L, Huber JA,et al. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing[J]. PLoS Genet, 2008, 4:e1000255. [6]Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities[J]. Appl Environ Microbial, 2009, 75(23):7537-7541. [7]Sun Y, Cai Y, Liu L, et al. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences[J]. Nucleic Acids Res, 2009, 37(10):e76. [8]Cai Y, Sun Y. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time[J]. Nucleic Acids Res, 2011, 39(14):e95. [9]Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences[J]. Bioinformatics,2006, 22(13): 1658-1659. [10]Edgar RC. Search and clustering orders of magnitude faster than BLAST[J]. Bioinformatics, 2010, 26(19):2460–2461. [11]Ghodsi M, Liu B, Pop M. DNACLUST: accurate and efficient clustering of phylogenetic marker genes[J]. BMC Bioinformatics, 2011, 12:1-11. [12]Hao X, Jiang R, Chen T. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering[J]. Bioinformatics, 2011, 27: 611–618. [13]Huse SM, Huber JA, Morrison HG, et al. Accuracy and quality of massively parallel DNA pyrosequencing[J]. Genome Biology, 2007, 8(7): R143. [14]Lysholm F, Andersson B, Persson B. An efficient simulator of 454 data using configurable statistical models[J]. BMC Research Notes, 2011, 4(1):449.    

服務與反饋:
文章下載】【加入收藏
提示:您還未登錄,請登錄!點此登錄
 
友情鏈接  
地址:北京安定門外安貞醫(yī)院內北京生物醫(yī)學工程編輯部
電話:010-64456508  傳真:010-64456661
電子郵箱:[email protected]