International Business Machines Corporation
Methods of automatically and self-consistently correcting genome databases

Abstract:

A method is described for automatically correcting metadata errors in a k-mer database. A k-mer database having a self-consistent taxonomy based on genome-genome distance was constructed from a set of sample and reference genomes whose metadata included taxonomic labeling from a reference taxonomy (the standard NCBI taxonomy), which is not based on genetic distance. As a result, genomes of a given taxonomic ID of the self-consistent taxonomy could be separated into clusters based on the differences in the metadata. Genomes of the clusters less than a minimum cluster size Cmin were removed and profiled against the remaining genomes, correcting metadata automatically for those genomes that could be mapped back. The resulting k-mer database showed improved specificity for genetic profiling. Another method is described for identifying and handling chimeric genomes using the self-consistent taxonomy. Another method is described for correcting a classification database.