ArticleMicrobiome2013
mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.
Article in Microbiome, 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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Who cites it
17 citing papers in PubMed.
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- CaptureSeq: Hybridization-Based Enrichment ofMicroorganisms · 2021Article
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- Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth.Microbiome · 2018Article
- Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.Applied and environmental microbiology · 2018Article
- The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women.Scientific reports · 2017Article
- Article
- A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.Microbiome · 2016Article
- Article
- NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.PLoS computational biology · 2016Article
- SPINGO: a rapid species-classifier for microbial amplicon sequences.BMC bioinformatics · 2015Article
- Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.BMC research notes · 2015Article
- Article
- ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences.BMC research notes · 2014Article
- Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds.The New phytologist · 2014Article
- Characterization of the fecal microbiota of pigs before and after inoculation with "Brachyspira hampsonii".PloS one · 2014Article
- Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle.Microbiome · 2014Article
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5 authors.
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Abstract
backgroundFormation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.
resultsHere we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.
conclusionsmPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
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