A novel algorithm for genomic STR mining: application to phylogeny reconstruction and taxa identification
by Uddalak Mitra; Soumya Majumder; Sayantan Bhowmick
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 20, No. 1, 2024

Abstract: With vast collection of whole genome data, analysts require faster and more scalable bioinformatics tools to compare those abundant sequences for knowledge discovery. Despite of their availability, utilising the larger whole genomes for phylogeny reconstruction and taxa identification is still a challenging task. In complex organisms, a substantial portion of genome is made up of repetitive DNA. The short tandem repeat (STR) is one of the most crucial repeats. We develop an efficient and scalable algorithm called STR seed selection (3S), which mines STRs in whole genomes using k-mer comparison. The analysis of short tandem repeats has revealed species-specific variations that serve as crucial indicators of their genetic relatedness. When it comes to reconstructing the phylogeny and identifying taxa within eukaryotic species, the utilisation of short tandem repeat variants consistently matches with the established taxonomy by NCBI. With its remarkable attributes of minimal memory usage, rapid processing capabilities, and exceptional scalability, 3S emerges as a cutting-edge approach for biosequence analysis based on short tandem repeats.

Online publication date: Thu, 14-Mar-2024

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