Introduction

Next-generation sequencing (NGS) technologies make it possible to obtain the entire genomic content of microorganisms in metagenome samples. Thus, many studies have developed methods for the processing and analysis of metagenomic NGS reads, including analyses for predicting functions and their enrichments in environmental metagenome samples. Especially, comparative functional studies by using multi-metagenome samples are essential for identifying and comparing different characteristics of multiple environmental samples. In this paper, we introduce a pipeline for functional characterization of multiple metagenome samples to infer major functions as well as their quantitative scores in a comparative metagenomics manner. The pipeline performs the annotation of functions related to expected proteins in the metagenome samples, calculates their enrichment scores based on the reads per kilobase per million reads (RPKM) measure, and predicts the relative abundance of associated functions by a statistical test. The results from single sample analysis are then used to find common and sample-specific major functions. By applying the pipeline to six different environmental metagenome samples, including two ocean (Antarctica aquatic and Baltic Sea) and four terrestrial (Acid mine drainage, human gut microbiome, Amazon River, and Wasca soil) samples, we were able to predict common functions as well as environment-specific functions. Our pipeline is available at http://bioinfo.konkuk.ac.kr/FCMM/.

Publications

  1. FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
    Cite this
    Lee J, Lee HT, Hong WY, Jang E, Kim J, 2015-08-01 - Journal of microbiological methods

Credits

  1. Jongin Lee
    Developer

    Department of Animal Biotechnology, Konkuk University

  2. Hoon Taek Lee
    Developer

    Department of Animal Biotechnology, Konkuk University

  3. Woon-young Hong
    Developer

    Department of Animal Biotechnology, Konkuk University

  4. Eunji Jang
    Developer

    Department of Animal Biotechnology, Konkuk University

  5. Jaebum Kim
    Investigator

    Department of Animal Biotechnology, Konkuk University

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Summary
AccessionBT001935
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByJaebum Kim