HTS (NGS) 関連のインフォマティクス情報についてまとめています。

16S/18S rRNAのV1~V9領域の配列を取り出す V-Xtractor


V-Xtractorは、隠れマルコフモデルを使用して、16S/18S rRNAの定義済みの超可変配列セグメント(V1〜V9)を検索、検証、および抽出する。99.6%の検出効率と低い偽陽性感受性により、このツールはデータの信頼性を向上させ、その後のコミュニティアッセイでの分析を容易にする。





  • Perl

  • 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).


git clone
cd V-Xtractor/


 > perl

$ perl 


V-Xtractor v. 2.0. Copyright (c) Hartmann et al. 2010.


Usage: [-a] [-b] [-d] [-e evalue] [-s score] [-r region] [-i (long|short)]

   [-h hmmdirectory] [-c csvoutput] [-o outputfile] inputfile [inputfiles...]


  This program will analyze each sequence in each input file, looking

  for the HMMs in the hmm directory.



    -o outputfile: Write the HMM region information to a FASTA file

    -c csvoutput: Write the HMM region information to a CSV file


    -h hmmdirectory: The directory containing HMM files named

       V[1-9]leftlong.HMM   V[1-9]leftshort.HMM

       V[1-9]rightlong.HMM  V[1-9]rightshort.HMM


    -r region: The regions to extract, in the following format:

      -r V1       -- the V1 region only

      -r .V1-V2.  -- the region from the left of V1 to the right of V2

      -r V1.-.V2  -- the region from the right of V1 to the left of V2

      -r .V3-.V7  -- the region from the left of V3 to the left of V7


    -i (long|short): Include HMM regions in the fasta output (default: exclude)

      The long or short HMM region will be chosen where applicable.


    -b: Use bitscore instead of evalue threshold (only use one or the other)

    -e evalue: Set the global evalue threshold (default: 0.01)

    -s score: Set the global score threshold (default: 0)


    -a: Check that HMMs occur in alphabetical order in each sequence


    Example: -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.



入力のSSU rRNA fastaを指定する。

perl -a -r V1-V3 -h HMMs/bacteria/ -o out.fasta in.fasta




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

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

Journal of Microbiological Methods
Volume 83, Issue 2, November 2010, Pages 250-253