About Microbiome Search Engine

Database Information

System version: 2.0

Search engine: Meta-Storms 2.2.1

Database information:


  • The standalone software (version std 2.2.1, lastest release: Jan. 4, 2019)
  • Linux X86_64 (bin package / src package)
  • Mac OS X (bin package / src package)
  • Here we provide a demo run with 20 human oral microbiome samples. This dataset has been integrated into the above packages.

    You can also get the latest release from Meta-Storms GitHub repository.

  • System requirement
  • Mac OS X needs to install the compiler that supports OpenMP by
    brew install gcc
  • Quick installation
  • Type the following commands in the directory that contains the package for quick installation:
    tar -xzvf meta-storms-2-std-2.2.1.tar.gz#Extract the package
    cd meta-storms#Go to the package directory
    source install.sh#Automatic installation
  • The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.
  • The sequence profiling software
  • We strongly recommend to use Parallel-META 3 for sequence profiling.
  • The QIIME 2 plugin
  • You can also get the QIIME 2 plugin of Meta-Storms 2 from q2-metastorms GitHub repository.
  • Supplementary
  • The test code and datasets for reproducing the results of manuscript "Model-free disease classification across cohorts via microbiome search" is available here (Linux X86_64 / Mac OS X, ~ 892 MB). See “Readme.txt” in the package for usage and details.


    1. X. Su*, G. Jing, D. McDonald, H. Wang, Z. Wang, A. Gonzalez, Z. Sun, S. Huang, J. Navas, R. Knight* and J. Xu*. Identifying and predicting novelty in microbiome studies, mBio, 2018. Link
    2. X.Su1, X. Wang1, G. Jing and K. Ning*. GPU-Meta-Storms: Computing the structure similarities among massive amount of microbial community samples using GPU, Bioinformatics, 2014. Link
    3. X. Su, J. Xu and K. Ning*. Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data, Bioinformatics, 2012. Link

Updatesmore >>

    1. Jan. 09, 2020. Due to system and database maintenance, MSE search service will be temporarily unstable during Jan. 09 - Jan. 10, 2020 (Beijing time). We are sorry for the inconvenience.
    2. Dec. 27, 2019. Now the MSE 2 is online, supporting OTU-based, species-based and KO-based search. MSE 2 provides both upload-based and paste-based query, and also enables the full-taxonomy multi-view of query and matches in search results.
    3. Dec. 26, 2019. The total number of samples in MSE has been updated to 235,743.
    4. Dec. 25, 2019. Due to system and database maintenance, MSE search service will be temporarily unstable during Dec 25- Dec 30, 2019 (Beijing time). We are sorry for the inconvenience.
    5. Dec 3, 2019. The Dynamic Meta-Storms algorithm for shotgun metagenomics comparison is published in Bioinformatics.

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