KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.

ABSTRACT: Genomic DNA is the best "unique identifier" for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification. Although this approach is not novel, selecting the appropriate k-mer length to obtain the optimal resolution is rather arbitrary. However, it is a very important parameter for achieving the appropriate resolution for genome/sequence distances to infer biologically meaningful phylogenetic relationships. Thus, there is a need for a systematic approach to identify the appropriate

SUBMITTER: Pornputtapong N 

PROVIDER: S-EPMC7538862 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature