Repository for V-Xtractor an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
Authors: Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH.
Published in: J Microbiol Methods. 2010 Nov;83(2):250-3. doi: 10.1016/j.mimet.2010.08.008. Epub 2010 Aug 27. V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.
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
Code is also hosted at Martin Hartmann's website: http://www.microbiome.ch/software Please contact him if you need more information, I was a postdoc in the lab where the tool was developed but I am not the owner of the code or the project.
Source code available at: http://www.cmde.science.ubc.ca/mohn/software.html
Version: 2.0 Purpose: Extraction of variable subregions from SSU rRNA sequences Copyright (c) Hartmann et al. 2010 University of British Columbia, Department of Microbiology and Immunology, V6T 1Z3 Vancouver, Canada Programmer: Charles Howes
The full installation instructions can be found in the file UsersGuide.pdf Quick installation instructions can be found below.
Perl is available at http://www.perl.org/
Installing HMMER version 3 note: V-Xtractor 2.0 requires HMMER version 3. An older version of V-Xtractor running on HMMER version 2 can be provided on request.
- Download http://hmmer.janelia.org/#download
- Uncompress/unpack tar zxf hmmer-3.0.tar.gz
- Move to new directory cd hmmer-3.0
- Configure ./configure
- Build make
- Automated tests make check
- Automated install make install
Precompiled binaries are available for some operating systems. Tdshey can be found in the "binaries/" directory after the unpacking the tarball. Installing the package takes nothing more than moving these binaries wherever you want them (e.g. /usr/local/bin).
- Download from http://www.cmde.science.ubc.ca/mohn/software.html or here https://github.com/carden24/V-Xtractor/blob/master/vxtractor.pl
Use sequences in FASTA formatted input file. Copy FASTA file to directory containing vxtractor.pl. Move into this directory with "cd path/". Typing "perl vxtractor.pl" lists all options of the program.
Example:perl vxtractor.pl -a -r .V1-V3. -h HMMs/bacteria/ -o out.fasta in.fasta -- this will extract V1 through V3, for bacteria, from the file in.fasta and save the results to out.fasta, checking correct order of V1, V2, and V3.