ArticleNucleic acids research2011
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins.Bioinformatics advances · 2026Article
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- CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats.Database : the journal of biological databases and curation · 2020Article
- The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules.International journal of molecular sciences · 2019Article
- A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator.Scientific data · 2018Article
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- De Novo characterization of transcriptomes from two North American Papaipema stem-borers (Lepidoptera: Noctuidae).PloS one · 2018Article
- Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake.Frontiers in microbiology · 2018Article
- Gene Unprediction with Spurio: A tool to identify spurious protein sequences.F1000Research · 2018Article
- The transcriptome of a "sleeping" invader: de novo assembly and annotation of the transcriptome of aestivating Cornu aspersum.BMC genomics · 2017Article
- rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
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- Microbiota diversity and gene expression dynamics in human oral biofilms.BMC genomics · 2014Article
- Article
- Comparative genomics of Blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome.Genome biology and evolution · 2013Article
- Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max.BMC plant biology · 2012Article
- Identification and removal of ribosomal RNA sequences from metatranscriptomes.Bioinformatics (Oxford, England) · 2012Article
- AntiFam: a tool to help identify spurious ORFs in protein annotation.Database : the journal of biological databases and curation · 2012Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In the course of analyzing 9,522,746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, 'Cw-hydrolase') uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.
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