Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.

ABSTRACT:

Background

A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a

SUBMITTER: Dubinkina VB 

PROVIDER: S-EPMC4715287 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature