期刊
PLOS ONE
卷 4, 期 12, 页码 -出版社
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0008230
关键词
-
资金
- College of Natural Resources and the Environment at the University of Massachusetts
- School of Medicine at the University of Michigan
- Sloan Foundation
- National Science Foundation [0743432]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [0743432] Funding Source: National Science Foundation
As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm. The purpose of this study was to create and validate an aligner with the goal of quickly generating a high quality alignment and having the flexibility to use any reference alignment. Using the simple nearest alignment space termination algorithm, the resulting aligner operates in linear time, requires a small memory footprint, and generates a high quality alignment. In addition, the alignments generated for variable regions were of as high a quality as the alignment of full-length sequences. As implemented, the method was able to align 18 full-length 16S rRNA gene sequences and 58 V2 region sequences per second to the 50,000-column SILVA reference alignment. Most importantly, the resulting alignments were of a quality equal to SILVA-generated alignments. The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule. Furthermore, because the implementation is not connected to a specific database it is easy to generalize the method to reference alignments for any DNA sequence.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据