Can you bank on GenBank

By D. Harris. 2003

219 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2c9c1b7f40dbb19f84ee4d20b762d8b71fbb7405

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Citations in the corpus

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. (2006, methodology): “…other tests of DNA barcoding and DNA taxonomy (e.g., Barrett and Hebert, 2005; Hebert et al, 2003b), we are here utilizing sequences from GenBank, although it is known to include misidentified sequences (e.g., Harris, 2003; Hebert et al., 2003b; Ruedas et al., 2000; Seberg, 2004; Vilgalys, 2003).”
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. (2012, background): “Several studies have reported on the various shortcomings of the public DNA sequence corpus (e.g., Gilks et al. 2002; Harris 2003; Bidartondo et al.”
DNA Barcodes for Marine Biodiversity: Moving Fast Forward? (2010, methodology): “These attributes make BOLD a more advantageous tool to use when dealing with DNA barcodes than GenBank (notorious for hosting erroneous data [32]), proved by an eight-fold amount of barcodes produced at BIO and directly stored in BOLD (>650,000 barcodes) compared to GenBank (>90,000 barcodes) (Febru”
Current progress in DNA barcoding and future implications for entomology (2011, background): “CBOL and the National Center for Biotechnology Information (NCBI) have already proposed a standard format (keyword “BARCODE”) for barcode sequences in GenBank (Consortium for the Barcode of Life 2005).”
What can biological barcoding do for marine biology? (2005, background): “Voucher specimens are not a requirement by GenBank today, which is a known problem as errors are frequently discovered in the submissions without any possibility of checking the original material (e.g. Harris 2003).”
Molecular identification of vertebrate species by oligonucleotide microarray in food and forensic samples (2008, background): “This case illustrates a more general problem, which is the reliability of sequences deposited in public databases (Harris 2003).”
DNA barcoding for ecologists. (2009, background): “However, the quality of the sequence data in GenBank, EMBL or DDBJ is not always perfect [ 11 ], either as a result of sequencing errors, contaminations, sample misidentifications or taxonomic problems.”
Molecular identification methods of fish species: reassessment and possible applications (2009, background): “In conclusion, Harris (2003) proposed several solutions to check the quality of the published sequences and the ‘‘simplest’’ is to re-sequence them.”
DNA barcoding detects market substitution in North American seafood (2008, background): “Unfortunately, given the present day torrent of data generation, erroneous records have been known to make their way into public archives (Bridges, Roberts, Spooner, & Panchal, 2003; Forster, 2003; Harris, 2003; Nilsson et al., 2006; Ross & Murugan, 2006; Yao, Bravi, & Bandelt, 2004).”
DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems (2019, unknown): “However, misidentifications of species are extensive (Harris, 2003).”
Vouchering DNA-barcoded specimens: test of a nondestructive extraction protocol for terrestrial arthropods (2007, background): “However, GenBank contains numerous errors, some of which are due to misidentification of the species whose DNA has been sequenced (Harris 2003; Vigalys 2003).”
Four priority areas to advance invasion science in the face of rapid environmental change (2020, background): “Two principal problems hinder molecular identifications: (i) accurate and complete barcoding of taxa across the taxonomic spectrum, and (ii) accurate and complete reference databases against which taxonomic assignments aremade (Harris 2003).”
The campaign to DNA barcode all fishes, FISH-BOL. (2009, background): “(2006) found that COI sequences generated only 70% success in species-level identification for Diptera using GenBank sequences, but many records in this repository are known to derive from misidentified specimens (Harris, 2003; Mitchell, 2008) and, or lack reference to the underlying specimens from ”
Who is eating what: diet assessment using next generation sequencing (2012, background): “wrong taxonomic assignations (Harris 2003).”
Effective monitoring of freshwater fish (2019, background): “Erroneous sequences and misidentifications are also frequent in GenBank and similar sequence databases (Harris, 2003).”
A large phylogeny of turtles (Testudines) using molecular data (2012, background): “Problems may arise from taxonomic misidentification (Vilgalys, 2003; Stuart and Fritz, 2008; Fritz et al., 2010), sequencing errors (Harris, 2003), and pseudogene amplification (Fritz et al., 2010).”