Alignment-free genomic sequence comparison using FCGR and signal processing.

ABSTRACT: BACKGROUND:Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing "nearby" species in a reference data set, or for constructing phylogenetic trees. RESULTS:We describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of

SUBMITTER: Lichtblau D 

PROVIDER: S-EPMC6937637 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature