TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

dc.contributor.author Brandt, Bernd W.
dc.contributor.author Bonder, Marc J.
dc.contributor.author Huse, Susan M.
dc.contributor.author Zaura, Egija
dc.date.accessioned 2013-02-06T16:51:02Z
dc.date.available 2013-02-06T16:51:02Z
dc.date.issued 2012-05-22
dc.description © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418. en_US
dc.description.abstract Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/. en_US
dc.description.sponsorship University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.). en_US
dc.format.mimetype application/pdf
dc.identifier.citation Nucleic Acids Research 40 (2012): W82-W87 en_US
dc.identifier.doi 10.1093/nar/gks418
dc.identifier.uri https://hdl.handle.net/1912/5748
dc.language.iso en_US en_US
dc.publisher Oxford University Press en_US
dc.relation.uri https://doi.org/10.1093/nar/gks418
dc.rights Attribution-NonCommercial 3.0 Unported *
dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0 *
dc.title TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage en_US
dc.type Article en_US
dspace.entity.type Publication
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relation.isAuthorOfPublication.latestForDiscovery 278c71ba-1d6e-46a9-873a-4c396b33766d
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