Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences
文献类型：期刊论文
| 作者 | Xiaoyu Wang; Yunpeng Cai; Yijun Sun; Rob Knight; Volker Mai |
| 刊名 | The ISME Journal
 |
| 出版日期 | 2012 |
| 英文摘要 | We would like to refute the suggestion that incorporating secondary structure information improves taxonomy-independent (TI; see Table 1 for list of abbreviations) 16S rRNA binning methods for partial 16S rRNA sequence reads. Although 16S rRNA secondary structure is crucial for its proper function, it is not clear that nucleotide differences at positions important for secondary structure contain unique phylogenetic information that requires different weighting than nucleotide differences at other positions. We support our position, and show the large computational expense required to include secondary structure information, using data from a simulation study. Our findings are important for microbial ecologists, as they confirm that an existing algorithm, ESPRIT-Tree (Cai and Sun, 2011), performs equally or better without consideration of secondary structure. Consequently, microbial ecologists who are already struggling with computational limitations analyzing vast data sets need not suspect that they are missing important improvements in operational taxonomic units (OTU) binning that could be achieved only at much greater computational cost, and can analyze data sets with many millions of sequences with confidence. |
| 收录类别 | 其他 |
| 原文出处 | http://www.nature.com/ismej/journal/v6/n7/pdf/ismej2011187a.pdf |
| 语种 | 英语 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/3980]  |
| 专题 | 深圳先进技术研究院_医工所 |
| 作者单位 | The ISME Journal |
| 推荐引用方式 GB/T 7714 | Xiaoyu Wang,Yunpeng Cai,Yijun Sun,et al. Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences[J]. The ISME Journal,2012. |
| APA | Xiaoyu Wang,Yunpeng Cai,Yijun Sun,Rob Knight,&Volker Mai.(2012).Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.The ISME Journal. |
| MLA | Xiaoyu Wang,et al."Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences".The ISME Journal (2012). |
入库方式： OAI收割
来源：深圳先进技术研究院
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