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Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons

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Metagenomic Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2649))

Abstract

Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.

Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers’ main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.

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Notes

  1. 1.

    https://www.bv-brc.org/

  2. 2.

    https://rdp.cme.msu.edu/classifier/classifier.jsp

  3. 3.

    http://pyro.cme.msu.edu/

  4. 4.

    https://usegalaxy.org/

  5. 5.

    http://kaiju.binf.ku.dk/server

  6. 6.

    https://phylopythias.bifo.helmholtz-hzi.de/index.php?phase=wait

  7. 7.

    https://www.mg-rast.org/

  8. 8.

    http://weizhong-lab.ucsd.edu/webMGA/

  9. 9.

    https://www.microbiomeanalyst.ca/

  10. 10.

    https://ruggleslab.shinyapps.io/wham_v1/

  11. 11.

    http://www.metagenassist.ca/

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Authors and Affiliations

  1. University of Science and Technology, Zewail City, Giza, Egypt

    Nehal Adel Abdelsalam

  2. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt

    Nehal Adel Abdelsalam

  3. Bioinformatics Group, Center for Informatics Sciences (CIS), Nile University, Giza, Egypt

    Hajar Elshora & Mohamed El-Hadidi

  4. Biomedical Informatics Program, School of Information Technology and Computer Science, Nile University, Giza, Egypt

    Hajar Elshora

Authors
  1. Nehal Adel Abdelsalam
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  2. Hajar Elshora
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  3. Mohamed El-Hadidi
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Correspondence to Mohamed El-Hadidi .

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Editors and Affiliations

  1. Leeds Institute of Medical Research, University of Leeds, Leeds, UK

    Suparna Mitra

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Abdelsalam, N.A., Elshora, H., El-Hadidi, M. (2023). Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons. In: Mitra, S. (eds) Metagenomic Data Analysis. Methods in Molecular Biology, vol 2649. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3072-3_7

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  • DOI: https://doi.org/10.1007/978-1-0716-3072-3_7

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