ArticleBioinformatics (Oxford, England)2015
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.Urolithiasis · 2024Article
- Multi-label classification with XGBoost for metabolic pathway prediction.BMC bioinformatics · 2024Article
- A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters.Scientific data · 2023Article
- Metagenome-Assembled Genome of a Putative Chemoheterotroph from Volcanic Terrain in Hawaii.Microbiology resource announcements · 2022Article
- Basaltic Lava Tube Hosts a Putative Novel Genus in the FamilyMicrobiology resource announcements · 2022Article
- Survival strategies of an anoxic microbial ecosystem in Lake Untersee, a potential analog for Enceladus.Scientific reports · 2022Article
- Metabolic pathway inference using multi-label classification with rich pathway features.PLoS computational biology · 2020Article
- Medium-Chain Fatty Acid Synthesis by "Applied and environmental microbiology · 2020Article
- An enzymatic pathway in the human gut microbiome that converts A to universal O type blood.Nature microbiology · 2019Article
- Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations.mSystems · 2019Article
- Article
- Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome.The ISME journal · 2018Article
- Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library.The Journal of biological chemistry · 2018Article
- Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant KelpFrontiers in microbiology · 2018Article
- Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment.PloS one · 2018Article
- Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.Nature communications · 2017Article
- Metabolic network analysis reveals microbial community interactions in anammox granules.Nature communications · 2017Article
- A geographically-diverse collection of 418 human gut microbiome pathway genome databases.Scientific data · 2017Article
- Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi.Frontiers in microbiology · 2017Article
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9 authors.
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Abstract
unlabelledNext-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. AVAILABILITY AND IMPLEMENTATION: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. CONTACT: shallam@mail.ubc.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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