A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA
Abstract Summary: 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 profile...
| Published in: | Bioinformatics |
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| Main Authors: | , |
| Format: | Article in Journal/Newspaper |
| Language: | English |
| Published: |
Oxford University Press (OUP)
2013
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| Subjects: | |
| Online Access: | http://dx.doi.org/10.1093/bioinformatics/btt254 https://academic.oup.com/bioinformatics/article-pdf/30/1/38/48913198/bioinformatics_30_1_38.pdf |
| Summary: | Abstract Summary: 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. Availability: PAUDA is freely available from: http://ab.inf.uni-tuebingen.de/software/pauda. Also supplementary method details are available from this website. Contact: daniel.huson@uni-tuebingen.de or xiechao@bic.nus.edu.sg |
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