Genome-wide search of nucleosome patterns using visual analytics.

ABSTRACT:

Motivation

The Burrows-Wheeler transform (BWT) is widely used for the fast alignment of high-throughput sequence data. This method also has potential applications in other areas of bioinformatics, and it can be specially useful for the fast searching of patterns on coverage data from different sources.

Results

We present a nucleosome pattern search method that converts levels of nucleosomal occupancy to a sequence-like format to which BWT searches can be applied. The method is embedded in a nucleosome map browser, 'Nucleosee', an interactive visual tool specifically designed to enhance BWT searches, giving them context and making them suitable for visual discourse analysis of the results. The proposed method is fast, flexible and sufficiently generic for the exploration of d

SUBMITTER: Santamaria R 

PROVIDER: S-EPMC6596885 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature