ArticleBioinformatics (Oxford, England)2013
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- The chromosome-level genome of Hemerocallis middendorffii provides new insights into the floral scents and color biosynthesis in Chinese native daylily.BMC plant biology · 2025Article
- TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.GigaScience · 2022Article
- Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme.Plant communications · 2022Article
- Gut Microbial Profile Is Associated With Residential Settings and Not Nutritional Status in Adults in Karnataka, India.Frontiers in nutrition · 2021Article
- DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data.Frontiers in genetics · 2021Article
- A high-quality genome provides insights into the new taxonomic status and genomic characteristics ofHorticulture research · 2020Article
- Assessing taxonomic metagenome profilers with OPAL.Genome biology · 2019Article
- A Bioinformatics Guide to Plant Microbiome Analysis.Frontiers in plant science · 2019Review
- Overview of Virus Metagenomic Classification Methods and Their Biological Applications.Frontiers in microbiology · 2018Review
- Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.Nature methods · 2017Article
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- Filtration and Normalization of Sequencing Read Data in Whole-Metagenome Shotgun Samples.PloS one · 2016Article
- Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.BMC bioinformatics · 2015Article
- Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.Bioinformatics (Oxford, England) · 2015Article
- UProC: tools for ultra-fast protein domain classification.Bioinformatics (Oxford, England) · 2015Article
- Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries.Microbiome · 2015Article
- Exploring neighborhoods in the metagenome universe.International journal of molecular sciences · 2014Article
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4 authors.
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Abstract
motivationMetagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases.
resultsWe introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure. AVAILABILITY: http://gobics.de/TaxyPro. SUPPLEMENTARY INFORMATION: Supplementary Material is available at Bioinformatics online.
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