ArticleBMC biology2015
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes.
Article in BMC biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection.Genome medicine · 2025Article
- Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.ISME communications · 2024Article
- ComammoxApplied and environmental microbiology · 2023Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds.Applied and environmental microbiology · 2021Article
- Article
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.eLife · 2020Article
- Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes.The ISME journal · 2020Article
- High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant.The ISME journal · 2020Article
- Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens.mSystems · 2020Article
- Genome Sequence of the Fish Brain Bacterium Clostridium tarantellae.Microbiology resource announcements · 2020Article
- Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics.Applied and environmental microbiology · 2019Article
- Characterisation of theFrontiers in microbiology · 2019Article
- Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production.Microbial cell factories · 2018Article
- Species-level functional profiling of metagenomes and metatranscriptomes.Nature methods · 2018Article
- Metagenomic Sequencing of Wastewater from a South African Research Farm.Microbiology resource announcements · 2018Article
- Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil.Genome announcements · 2018Article
- GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.Nucleic acids research · 2018Article
- Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses.Microbiome · 2018Article
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomes provide access to the taxonomic composition and functional capabilities of microbial communities. Although metagenomic analysis methods exist for estimating overall community composition or metabolic potential, identifying specific taxa that encode specific functions or pathways of interest can be more challenging. Here we present MetAnnotate, which addresses the common question: "which organisms perform my function of interest within my metagenome(s) of interest?" MetAnnotate uses profile hidden Markov models to analyze shotgun metagenomes for genes and pathways of interest, classifies retrieved sequences either through a phylogenetic placement or best hit approach, and enables comparison of these profiles between metagenomes.
resultsBased on a simulated metagenome dataset, the tool achieves high taxonomic classification accuracy for a broad range of genes, including both markers of community abundance and specific biological pathways. Lastly, we demonstrate MetAnnotate by analyzing for cobalamin (vitamin B12) synthesis genes across hundreds of aquatic metagenomes in a fraction of the time required by the commonly used Basic Local Alignment Search Tool top hit approach.
conclusionsMetAnnotate is multi-threaded and installable as a local web application or command-line tool on Linux systems. Metannotate is a useful framework for general and/or function-specific taxonomic profiling and comparison of metagenomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.