Detecting epigenetic motifs in low coverage and metagenomics settings.

ABSTRACT:

Background

It has recently become possible to rapidly and accurately detect epigenetic signatures in bacterial genomes using third generation sequencing data. Monitoring the speed at which a single polymerase inserts a base in the read strand enables one to infer whether a modification is present at that specific site on the template strand. These sites can be challenging to detect in the absence of high coverage and reliable reference genomes.

Methods

Here we provide a new method for detecting epigenetic motifs in bacteria on datasets with low-coverage, with incomplete references, and with mixed samples (i.e. metagenomic data). Our approach treats motif inference as a kmer comparison problem. First, genomes (or contigs) are deconstructed into kmers. Then, native genome-wide

SUBMITTER: Beckmann ND 

PROVIDER: S-EPMC4168715 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature