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

Ri Na You, Woo Chan Kim, Kang Hoon Lee, Young Kwan Lee, Kyung Seop Shin, Kiho Cho, Dong Ho Cho

Research output: Contribution to journalArticle

2 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)209-214
Number of pages6
JournalGenomics
Volume102
Issue number4
DOIs
StatePublished - Oct 2013

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Keywords

  • Linear visualization
  • RE array
  • REMiner
  • RepeatMasker
  • Repetitive element
  • Repetitive element array

ASJC Scopus subject areas

  • Genetics

Cite this

You, R. N., Kim, W. C., Lee, K. H., Lee, Y. K., Shin, K. S., Cho, K., & Cho, D. H. (2013). REViewer: A tool for linear visualization of repetitive elements within a sequence query. Genomics, 102(4), 209-214. https://doi.org/10.1016/j.ygeno.2013.07.008