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- Title
A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.
- Authors
Huson, Daniel H; Xie, Chao
- Abstract
In the context of metagenomics, we introduce a new approach to protein database search called PAUDA, which runs ~10,000 times faster than BLASTX, while achieving about one-third of the assignment rate of reads to KEGG orthology groups, and producing gene and taxon abundance profiles that are highly correlated to those obtained with BLASTX. PAUDA requires <80 CPU hours to analyze a dataset of 246 million Illumina DNA reads from permafrost soil for which a previous BLASTX analysis (on a subset of 176 million reads) reportedly required 800,000 CPU hours, leading to the same clustering of samples by functional profiles.
- Publication
Bioinformatics (Oxford, England), 2014, Vol 30, Issue 1, p38
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btt254