Identification and removal of ribosomal RNA sequences from metatranscriptomes

被引：166

作者：

Schmieder, Robert ^{[1
,2
]}

Lim, Yan Wei ^{[3
]}

Edwards, Robert ^{[1
,4
]}

机构：

[1] San Diego State Univ, Dept Comp Sci, San Diego, CA 92182 USA

[2] San Diego State Univ, Computat Sci Res Ctr, San Diego, CA 92182 USA

[3] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA

[4] Argonne Natl Lab, Math & Comp Sci Div, Argonne, IL 60439 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 03期

基金：

美国国家科学基金会;

关键词：

MICROBIAL METATRANSCRIPTOMICS; RAST SERVER; RESOURCE; DATABASE; PROJECT; ARB;

D O I：

10.1093/bioinformatics/btr669

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Here, we present riboPicker, a robust framework for the rapid, automated identification and removal of ribosomal RNA sequences from metatranscriptomic datasets. The results can be exported for subsequent analysis, and the databases used for the web-based version are updated on a regular basis. riboPicker categorizes rRNA-like sequences and provides graphical visualizations and tabular outputs of ribosomal coverage, alignment results and taxonomic classifications. Availability and implementation: This open-source application was implemented in Perl and can be used as stand-alone version or accessed online through a user-friendly web interface. The source code, user help and additional information is available at http://ribopicker.sourceforge.net/.

引用

页码：433 / 435

页数：3

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