REViewer: A tool for linear visualization of repetitive elements within a sequence query

Abstract

A species-specific population of arrangements of repetitive elements (REs), called RE arrays, exists in the human and mouse genomes. We developed an RE analytical tool, named REViewer, for visualizing RE occurrences within RE arrays and other genomic regions as an interactive line map. REViewer utilizes an RE reference library which is established with two RE types: 1) REMiner-generated undefined REs and 2) RepeatMasker-derived defined REs. RE occurrences within queries are visualized as a line map using these two RE types. The REViewer's controller provides analytical options, such as zoom, customization of axis unit, and RE type selection. The functionality of REViewer was evaluated using the human chromosome Y sequence. The REViewer is determined to be an efficient tool that facilitates visualization of up to 6000 REs in RE arrays and other genomic regions. The maximum query size is linked to the RE mining tools (e.g., REMiner, RepeatMasker), not to REViewer. (C) 2013 Elsevier Inc. All rights reserved.