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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

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V-Xtractor

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.

Requirements

Perl and HMMER

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).

Running V-Xtractor

Input file and running V-Xtractor

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.

We have included all the Hidden Markov models for the different regoions in this compressed file https://github.com/carden24/V-Xtractor/blob/master/HMMs.zip

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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

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