macでインフォマティクス

macでインフォマティクス

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。

 

インストール

ubuntu16.04でテストした。

依存

  • 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).

Github

git clone https://github.com/carden24/V-Xtractor.git
cd V-Xtractor/

#HMMファイルの解凍
unzip HMMs.zip

 > perl vxtractor.pl

$ perl vxtractor.pl 

 

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

 

Usage: vxtractor.pl [-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.

 

  Options:

    -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:

    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.

 

実行方法

入力のSSU rRNA fastaを指定する。

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

 

 

引用

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