Advertisement

The Application of DDCA to Metagenomic Analysis

  • Kazutoshi Yoshitake
  • Kyohei Matsuno
  • Atsumi TsujimotoEmail author
Chapter

Abstract

With the advent of the next-generation sequencer (NGS), sequencing costs have dramatically declined, but data analysis still costs as much as before or more. One of the reasons is that for NGS data analysis, it is necessary to key in commands on Linux which is a less common operating system. Therefore, we have developed the digital DNA chip analysis (DDCA) system which processes NGS data to produce results similar to microarray that are familiar to wet researchers. With this system, it is not necessary to have a high-performance computer in the laboratory, and analysis can be performed by using simple mouse operations on a web browser. After uploading sequence data to our server, users can click on some options to perform an analysis called digital hybridization on DDCA. In this paper, after describing the DDCA system, we introduce the procedure to analyze metagenome data using actual sequence data.

Keywords

DDCA Digital hybridization Digital DNA chip Visualization 

References

  1. Iwasaki W et al (2013 Nov) Mol Biol Evol 30(11):2531–2540.  https://doi.org/10.1093/molbev/mst141 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Miya M et al (2015) R Soc Open Sci 2(7):150088.  https://doi.org/10.1098/rsos.150088 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Nielsen HB et al (2014) Nat Biotechnol 32(8):822–828.  https://doi.org/10.1038/nbt.2939 CrossRefPubMedGoogle Scholar
  4. Skinner ME et al (2009) Genome Res 19(9):1630–1638.  https://doi.org/10.1101/gr.094607.109 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Kazutoshi Yoshitake
    • 1
  • Kyohei Matsuno
    • 1
  • Atsumi Tsujimoto
    • 1
    Email author
  1. 1.Japan Software Management Co., Ltd.Kanagawa-ku Yokohama-shiJapan

Personalised recommendations