New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras
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Summary
A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts, which far exceed previous estimates of artifacts within public repositories and highlight the urgent need for all researchers to adequately screen their libraries prior to submission.
- Type
- article
- Published
- 2006-09-01
- Cited by
- 722
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W2061559511
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:17486495
Keywords
16S ribosomal RNA, Phylogenetic tree, clone (Java method), Biology, Mega-
References
- Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem.
- DNA damage promotes jumping between templates during enzymatic amplification.
- Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms
- Bacterial community in sediment from the Western Pacific “Warm Pool” and its relationship to environment
- Obesity alters gut microbial ecology.
- Microbes on the human vaginal epithelium
- Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees.
- Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea
- The Distribution of Microbial Taxa in the Subsurface Water of the Kalahari Shield, South Africa
- Geobiology of a microbial endolithic community in the Yellowstone geothermal environment
- The Effect of Protozoa on the Composition of Rumen Bacteria in Cattle Using 16S rRNA Gene Clone Libraries
- Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments.
- Distribution and culturability of the uncultivated 'AGG58 cluster' of the Bacteroidetes phylum in aquatic environments.
- Hybrid DNA artifact from PCR of closely related target sequences.
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
- Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes
- Synchrony and seasonality in bacterioplankton communities of two temperate rivers
- Comparative Metagenomics of Microbial Communities
- Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.
- Phylogenetic Characterization of a Polychlorinated-Dioxin- Dechlorinating Microbial Community by Use of Microcosm Studies
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- Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary)
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