V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16 S/18 S) ribosomal RNA gene sequences

被引：92

作者：

Hartmann, Martin ^{[1
]}

Howes, Charles G. ^{[1
]}

Abarenkov, Kessy ^{[2
]}

Mohn, William W. ^{[1
]}

Nilsson, R. Henrik ^{[2
,3
]}

机构：

[1] Univ British Columbia, Dept Microbiol & Immunol, Inst Life Sci, Vancouver, BC V5Z 1M9, Canada

[2] Univ Tartu, Dept Bot, Inst Ecol & Earth Sci, EE-50090 Tartu, Estonia

[3] Univ Gothenburg, Dept Plant & Environm Sci, Gothenburg, Sweden

来源：

JOURNAL OF MICROBIOLOGICAL METHODS | 2010年 / 83卷 / 02期

关键词：

Software; SSU rRNA sequences; Hypervariable regions; High-throughput sequencing; Hidden Markov Models; HMMER; COMMUNITIES; DATABASE; GENERATION; SPACE; SEA; ARB;

D O I：

10.1016/j.mimet.2010.08.008

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to false-positives, this tool refines data reliability and facilitates subsequent analysis in community assays. (C) 2010 Elsevier B.V. All rights reserved.

引用

页码：250 / 253

页数：4

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