At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies

By K. Ashelford, N. Chuzhanova, J. Fry, Antonia J. Jones, A. Weightman. Applied and Environmental Microbiology, 2005

827 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/720fa0fc245184a4809f1e45f2629e22888241bf

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Citations in the corpus

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB (2007, methodology): “nuc_gene_slv Aligned bases within gene boundaries pintail_slv Information about potential sequence anomalies detected by Pintail (22); 100 means no anomalies found.”
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease (2011, methodology): “Sequences were tested for chimeras with Mallard [79], Bellerophon at Greengenes [77] and Pintail [ 80 ] and any that appeared to be chimeric were removed.”
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls (2007, background): “Much of this misinformation that was originally present in such databases was thought to have been corrected; however, a recent multicenter study from the United Kingdom (1) conservatively estimates that at least 5% of the 1,399 sequences searched had substantial errors associated with them ranging ”
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification (2008, background): “2006) and that there are other compounding factors such as chimeric sequences and obsolete classifi cation systems and synonyms (Ashelford et al. 2005; Bidartondo et al. 2008; Ryberg et al. 2008) that render diffi cult the extrication of true taxonomic signal from the welter of noise surrounding it.”
A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales (2009, methodology): “Once Deviation from Expectation (DE) values were calculated for each sequence (using the Pintail algorithm; Ashelford et al., 2005) and plotted against mean percentage difference values, outlier DE values were identified using a raw data quantile plot (derived from analyses of type strain sequences ”
Early marine bacterial biofilm on a copper-based antifouling paint (2013, neutral): “, 2005) and Pintail (Ashelford et al., 2005).”
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007, methodology): “The files were then tested for the presence of chimeric sequences using Mallard [52] and Bellerophon [55], and putative chimeras were checked using Pintail [56] and BLAST [57].”
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies (2011, methodology): “First, Haas and colleagues [21] developed the ChimeraSlayer algorithm, which they showed to be superior to Bellerephon [30] and Pintail [31], especially for short sequences and in cases where the parents of the chimera were closely related to each other.”
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006, methodology): “As a major quality improvement, all sequences are now tested for sequence anomalies, including chimeric sequence anomalies, using Pintail from the Cardiff Bioinformatics Toolkit ( 4 ).”
Anaerobic biodegradation of crude oil under sulphate-reducing conditions leads to only modest enrichment of recognized sulphate-reducing taxa (2013, neutral): “0 (Ashelford et al., 2005), and removed from subsequent analyses.”
Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge (2009, methodology): “(1998) followed by an analysis with the Pintail tool which compares the sequences with a set of reference to identify chimeras (Ashelford et al., 2005).”
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (2011, methodology): “To evaluate the Pintail algorithm and to obtain a version of the software that was both compatible with NAST-alignments and for use in a high-throughput environment, we reimplemented the algorithm as previously described (Ashelford et al. 2005).”
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008, methodology): “As described in our previous update (1), all sequences are tested for anomalies using the Pintail program (2).”