A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA
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 ar...
| Published in: | Bioinformatics |
|---|---|
| Main Authors: | , |
| Format: | Text |
| Language: | English |
| Published: |
Oxford University Press
2014
|
| Subjects: | |
| Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866550 http://www.ncbi.nlm.nih.gov/pubmed/23658416 https://doi.org/10.1093/bioinformatics/btt254 |
| _version_ | 1821682214989987840 |
|---|---|
| author | Huson, Daniel H. Xie, Chao |
| author_facet | Huson, Daniel H. Xie, Chao |
| author_sort | Huson, Daniel H. |
| collection | PubMed Central (PMC) |
| container_issue | 1 |
| container_start_page | 38 |
| container_title | Bioinformatics |
| container_volume | 30 |
| description | 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. |
| format | Text |
| genre | permafrost |
| genre_facet | permafrost |
| id | ftpubmed:oai:pubmedcentral.nih.gov:3866550 |
| institution | Open Polar |
| language | English |
| op_collection_id | ftpubmed |
| op_container_end_page | 39 |
| op_doi | https://doi.org/10.1093/bioinformatics/btt254 |
| op_relation | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866550 http://www.ncbi.nlm.nih.gov/pubmed/23658416 http://dx.doi.org/10.1093/bioinformatics/btt254 |
| op_rights | © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| op_rightsnorm | CC-BY |
| publishDate | 2014 |
| publisher | Oxford University Press |
| record_format | openpolar |
| spelling | ftpubmed:oai:pubmedcentral.nih.gov:3866550 2025-01-17T00:16:04+00:00 A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA Huson, Daniel H. Xie, Chao 2014-01-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866550 http://www.ncbi.nlm.nih.gov/pubmed/23658416 https://doi.org/10.1093/bioinformatics/btt254 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866550 http://www.ncbi.nlm.nih.gov/pubmed/23658416 http://dx.doi.org/10.1093/bioinformatics/btt254 © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY Hitseq Papers Text 2014 ftpubmed https://doi.org/10.1093/bioinformatics/btt254 2013-12-22T01:52:42Z 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. Text permafrost PubMed Central (PMC) Bioinformatics 30 1 38 39 |
| spellingShingle | Hitseq Papers Huson, Daniel H. Xie, Chao A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title | A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title_full | A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title_fullStr | A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title_full_unstemmed | A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title_short | A poor man’s BLASTX—high-throughput metagenomic protein database search using PAUDA |
| title_sort | poor man’s blastx—high-throughput metagenomic protein database search using pauda |
| topic | Hitseq Papers |
| topic_facet | Hitseq Papers |
| url | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866550 http://www.ncbi.nlm.nih.gov/pubmed/23658416 https://doi.org/10.1093/bioinformatics/btt254 |