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 Citations (Scopus)

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

Fingerprint

Chromosomes, Human, Y
Human Genome
Libraries
Population

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

REViewer : A tool for linear visualization of repetitive elements within a sequence query. / You, Ri Na; Kim, Woo Chan; Lee, Kang Hoon; Lee, Young Kwan; Shin, Kyung Seop; Cho, Kiho; Cho, Dong Ho.

In: Genomics, Vol. 102, No. 4, 10.2013, p. 209-214.

Research output: Contribution to journalArticle

You, Ri Na ; Kim, Woo Chan ; Lee, Kang Hoon ; Lee, Young Kwan ; Shin, Kyung Seop ; Cho, Kiho ; Cho, Dong Ho. / REViewer : A tool for linear visualization of repetitive elements within a sequence query. In: Genomics. 2013 ; Vol. 102, No. 4. pp. 209-214.
@article{c3c2e98b9afa426195f2fbfa20255009,
title = "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.",
keywords = "Linear visualization, RE array, REMiner, RepeatMasker, Repetitive element, Repetitive element array",
author = "You, {Ri Na} and Kim, {Woo Chan} and Lee, {Kang Hoon} and Lee, {Young Kwan} and Shin, {Kyung Seop} and Kiho Cho and Cho, {Dong Ho}",
year = "2013",
month = "10",
doi = "10.1016/j.ygeno.2013.07.008",
language = "English (US)",
volume = "102",
pages = "209--214",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - REViewer

T2 - A tool for linear visualization of repetitive elements within a sequence query

AU - You, Ri Na

AU - Kim, Woo Chan

AU - Lee, Kang Hoon

AU - Lee, Young Kwan

AU - Shin, Kyung Seop

AU - Cho, Kiho

AU - Cho, Dong Ho

PY - 2013/10

Y1 - 2013/10

N2 - 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.

AB - 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.

KW - Linear visualization

KW - RE array

KW - REMiner

KW - RepeatMasker

KW - Repetitive element

KW - Repetitive element array

UR - http://www.scopus.com/inward/record.url?scp=84886298175&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84886298175&partnerID=8YFLogxK

U2 - 10.1016/j.ygeno.2013.07.008

DO - 10.1016/j.ygeno.2013.07.008

M3 - Article

VL - 102

SP - 209

EP - 214

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 4

ER -