A high-throughput DNA sequence aligner for microbial ecology studies

• Published in: PloS one 2009-12, Vol.4 (12), p.e8230-e8230
• Main Author: Schloss, Patrick D
• Format: Article
• Language: English
• Subjects: Algorithms; Alignment; Analysis; Antibiotics; Bacteria - genetics; Base Sequence; Columns (structural); Computational Biology/Genomics; Computational Biology/Metagenomics; Computer science; Data analysis; Data processing; Databases, Nucleic Acid; Datasets; Deoxyribonucleic acid; DNA; DNA sequencing; Ecological and Environmental Phenomena; Ecological monitoring; Ecology; Gene sequencing; High-Throughput Screening Assays - instrumentation; Information management; Metabolism; Microbiology/Environmental Microbiology; Microorganisms; Molecular Sequence Data; Molecular structure; Nucleotide sequence; Protein structure; RNA; rRNA 16S; Secondary structure; Sequence Alignment - instrumentation; Sequence Analysis, DNA - instrumentation; Surveys
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0008230

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.