ArticleBMC bioinformatics2011
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Heat stress and the chicken gastrointestinal microbiota: a systematic review.Journal of animal science and biotechnology · 2025Review
- RFW captures species-level metagenomic functions by integrating genome annotation information.Cell reports methods · 2024Article
- The dynamics of the midgut microbiome inPNAS nexus · 2024Article
- Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain.Nature microbiology · 2023Article
- Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland.Archives of microbiology · 2023Article
- 'Multi-omics' data integration: applications in probiotics studies.NPJ science of food · 2023Review
- Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis.Microorganisms · 2021Review
- The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3.Viruses · 2021Article
- Article
- Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota.Environmental microbiology · 2020Article
- Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture.Frontiers in microbiology · 2019Article
- Diabetes-associated alterations in the cecal microbiome and metabolome are independent of diet or environment in the UC Davis Type 2 Diabetes Mellitus Rat model.American journal of physiology. Endocrinology and metabolism · 2018Article
- Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal.Environmental science and pollution research international · 2018Article
- Metatranscriptomics analysis of cyanobacterial aggregates during cyanobacterial bloom period in Lake Taihu, China.Environmental science and pollution research international · 2018Article
- Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.BioMed research international · 2018Article
- Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas.BMC systems biology · 2017Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of metagenome projects. While metagenomics provides information on the gene content, metatranscriptomics aims at understanding gene expression patterns in microbial communities. The initial computational analysis of a metagenome or metatranscriptome addresses three questions: (1) Who is out there? (2) What are they doing? and (3) How do different datasets compare? There is a need for new computational tools to answer these questions. In 2007, the program MEGAN (MEtaGenome ANalyzer) was released, as a standalone interactive tool for analyzing the taxonomic content of a single metagenome dataset. The program has subsequently been extended to support comparative analyses of multiple datasets.
resultsThe focus of this paper is to report on new features of MEGAN that allow the functional analysis of multiple metagenomes (and metatranscriptomes) based on the SEED hierarchy and KEGG pathways. We have compared our results with the MG-RAST service for different datasets.
conclusionsThe MEGAN program now allows the interactive analysis and comparison of the taxonomical and functional content of multiple datasets. As a stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.
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