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Updated: Feb 3, 2026

DNA-based Fish Species Identification Protocol
Published on: April 28, 2010
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Daniel J Nasko1, Sergey Koren2, Adam M Phillippy2
1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
Abstract:
In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.
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