Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.

ABSTRACT: We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for compu

SUBMITTER: Sarkar BK 

PROVIDER: S-EPMC8249421 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature