A high-throughput DNA sequence aligner for microbial ecology studies.

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 gen

SUBMITTER: Schloss PD 

PROVIDER: S-EPMC2788221 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature