V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.
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.
Hartmann
Martin
M
Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada. martinha@interchange.ubc.ca
Howes
Charles G
CG
Abarenkov
Kessy
K
Mohn
William W
WW
Nilsson
R Henrik
RH
D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005658:Fungi / Q000145:classification* / Q000235:genetics; D005827:Genetics, Microbial / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D011110:Polymorphism, Genetic; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D012984:Software
D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004271:DNA, Fungal; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S