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Methods in molecular biology (Clifton, N.J.)
2023;2649 133-174.

Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.

Nehal Adel Abdelsalam, Hajar Elshora, Mohamed El-Hadidi
Author Information
  1. Nehal Adel Abdelsalam: University of Science and Technology, Zewail City, Giza, Egypt.
  2. Hajar Elshora: Bioinformatics Group, Center for Informatics Sciences (CIS), Nile University, Giza, Egypt.
  3. Mohamed El-Hadidi: Bioinformatics Group, Center for Informatics Sciences (CIS), Nile University, Giza, Egypt. melhadidi@nu.edu.eg.
PMID: 37258861 DOI: 10.1007/978-1-0716-3072-3_7

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.

Keywords

Functional metagenomics Metagenomics Shotgun sequencing Taxonomy Web tools

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MeSH Term

Metagenomics
Metagenome
Microbiota
Ecology
Computational Biology
Data Analysis
Journal Article

Word Cloud

Created with Highcharts 10.0.0metagenomicdatatoolssequencinganalysisfunctionalresearchpotentialecosystemsMetagenomicscompositionmicrobialmetagenomicsRecentlytechnologiesbecomereadilyavailablescientistsmotivatedconductunveilmyriadbiomesstudiesfunctionscommunitiespaveswaymultipleapplicationsmedicineindustryecologyNonethelessimmenseamountuser-friendlypipelinescarrynewchallengeWeb-basedbioinformaticsnowdevelopedfacilitatecomplexwithoutpriorknowledgeprogramminglanguagesspecialinstallationSpecializedwebhelpanswerresearchers'mainquestionstaxonomicclassificationcapabilitiesdiscrepanciestwoprobablecorrelationsmembersspecificcommunityInternetconnectionclicksresearcherscanconvenientlyefficientlyanalyzedatasetssummarizeresultsvisualizekeyinformationsamplesstudychapterprovidessimpleguidefundamentalweb-basedservicesusedanalysesBV-BRCRDPMG-RASTMicrobiomeAnalystMETAGENassistMGnifyInteractiveWeb-BasedServicesMetagenomicDataAnalysisComparisonsFunctionalShotgunTaxonomyWeb

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