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

Martin Hartmann; Charles G Howes; Kessy Abarenkov; William W Mohn; R Henrik Nilsson

doi:10.1016/j.mimet.2010.08.008

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

J Microbiol Methods. 2010 Nov;83(2):250-3. doi: 10.1016/j.mimet.2010.08.008. Epub 2010 Aug 27.

Authors

Martin Hartmann¹, Charles G Howes, Kessy Abarenkov, William W Mohn, R Henrik Nilsson

Affiliation

¹ Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada. [email protected]

PMID: 20804791
DOI: 10.1016/j.mimet.2010.08.008

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Archaea / classification*
Archaea / genetics
Bacteria / classification*
Bacteria / genetics
DNA, Archaeal / genetics
DNA, Bacterial / genetics
DNA, Fungal / genetics
DNA, Ribosomal / genetics
Fungi / classification*
Fungi / genetics
Genetics, Microbial / methods*
High-Throughput Nucleotide Sequencing / methods
Polymorphism, Genetic
RNA, Ribosomal, 16S / genetics*
RNA, Ribosomal, 18S / genetics*
Software*

Substances

DNA, Archaeal
DNA, Bacterial
DNA, Fungal
DNA, Ribosomal
RNA, Ribosomal, 16S
RNA, Ribosomal, 18S