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A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

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  • Patrick D Schloss

Abstract

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.

Suggested Citation

  • Patrick D Schloss, 2009. "A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies," PLOS ONE, Public Library of Science, vol. 4(12), pages 1-9, December.
  • Handle: RePEc:plo:pone00:0008230
    DOI: 10.1371/journal.pone.0008230
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    1. Peter J. Turnbaugh & Micah Hamady & Tanya Yatsunenko & Brandi L. Cantarel & Alexis Duncan & Ruth E. Ley & Mitchell L. Sogin & William J. Jones & Bruce A. Roe & Jason P. Affourtit & Michael Egholm & Be, 2009. "A core gut microbiome in obese and lean twins," Nature, Nature, vol. 457(7228), pages 480-484, January.
    2. Les Dethlefsen & Sue Huse & Mitchell L Sogin & David A Relman, 2008. "The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing," PLOS Biology, Public Library of Science, vol. 6(11), pages 1-18, November.
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    1. Jarrod J Scott & John A Breier & George W Luther III & David Emerson, 2015. "Microbial Iron Mats at the Mid-Atlantic Ridge and Evidence that Zetaproteobacteria May Be Restricted to Iron-Oxidizing Marine Systems," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-19, March.
    2. Shuan Jia & Yongcheng Chen & Rongzheng Huang & Yuxin Chai & Chunhui Ma & Fanfan Zhang, 2023. "Study on Phyllosphere Microbial Community of Nettle Leaf during Different Seasons," Agriculture, MDPI, vol. 13(6), pages 1-15, June.

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