ArticleBioinformatics (Oxford, England)2015
UProC: tools for ultra-fast protein domain classification.
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 46 papers.
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46 citing papers in PubMed.
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- Exploring changes in bacterioplankton community structure in response to tannic acid, a major component of mangrove litterfall of Sundarbans mangrove ecosystem: a laboratory mesocosm approach.Environmental science and pollution research international · 2022Article
- Improving protein domain classification for third-generation sequencing reads using deep learning.BMC genomics · 2021Article
- Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean.The ISME journal · 2021Article
- Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities.Frontiers in microbiology · 2021Article
- Gut Microbial Profile Is Associated With Residential Settings and Not Nutritional Status in Adults in Karnataka, India.Frontiers in nutrition · 2021Article
- Metformin elicits antitumour effect by modulation of the gut microbiota and rescues Fusobacterium nucleatum-induced colorectal tumourigenesis.EBioMedicine · 2020Article
- Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction.Investigative ophthalmology & visual science · 2020Article
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1 author.
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Abstract
motivationWith rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics.
resultsThe ultrafast protein classification (UProC) toolbox implements a novel algorithm ('Mosaic Matching') for large-scale sequence analysis. UProC is by three orders of magnitude faster than profile-based methods and in a metagenome simulation study achieved up to 80% higher sensitivity on unassembled 100 bp reads. AVAILABILITY AND IMPLEMENTATION: UProC is available as an open-source software at https://github.com/gobics/uproc. Precompiled databases (Pfam) are linked on the UProC homepage: http://uproc.gobics.de/. CONTACT: peter@gobics.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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