Cargando…

Meander: visually exploring the structural variome using space-filling curves

The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structu...

Descripción completa

Detalles Bibliográficos
Autores principales: Pavlopoulos, Georgios A., Kumar, Parveen, Sifrim, Alejandro, Sakai, Ryo, Lin, Meng Lay, Voet, Thierry, Moreau, Yves, Aerts, Jan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675473/
https://www.ncbi.nlm.nih.gov/pubmed/23605045
http://dx.doi.org/10.1093/nar/gkt254
_version_ 1782476098255192064
author Pavlopoulos, Georgios A.
Kumar, Parveen
Sifrim, Alejandro
Sakai, Ryo
Lin, Meng Lay
Voet, Thierry
Moreau, Yves
Aerts, Jan
author_facet Pavlopoulos, Georgios A.
Kumar, Parveen
Sifrim, Alejandro
Sakai, Ryo
Lin, Meng Lay
Voet, Thierry
Moreau, Yves
Aerts, Jan
author_sort Pavlopoulos, Georgios A.
collection PubMed
description The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander.
format Online
Article
Text
id pubmed-3675473
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-36754732013-06-07 Meander: visually exploring the structural variome using space-filling curves Pavlopoulos, Georgios A. Kumar, Parveen Sifrim, Alejandro Sakai, Ryo Lin, Meng Lay Voet, Thierry Moreau, Yves Aerts, Jan Nucleic Acids Res Methods Online The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander. Oxford University Press 2013-06 2013-04-19 /pmc/articles/PMC3675473/ /pubmed/23605045 http://dx.doi.org/10.1093/nar/gkt254 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Pavlopoulos, Georgios A.
Kumar, Parveen
Sifrim, Alejandro
Sakai, Ryo
Lin, Meng Lay
Voet, Thierry
Moreau, Yves
Aerts, Jan
Meander: visually exploring the structural variome using space-filling curves
title Meander: visually exploring the structural variome using space-filling curves
title_full Meander: visually exploring the structural variome using space-filling curves
title_fullStr Meander: visually exploring the structural variome using space-filling curves
title_full_unstemmed Meander: visually exploring the structural variome using space-filling curves
title_short Meander: visually exploring the structural variome using space-filling curves
title_sort meander: visually exploring the structural variome using space-filling curves
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675473/
https://www.ncbi.nlm.nih.gov/pubmed/23605045
http://dx.doi.org/10.1093/nar/gkt254
work_keys_str_mv AT pavlopoulosgeorgiosa meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT kumarparveen meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT sifrimalejandro meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT sakairyo meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT linmenglay meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT voetthierry meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT moreauyves meandervisuallyexploringthestructuralvariomeusingspacefillingcurves
AT aertsjan meandervisuallyexploringthestructuralvariomeusingspacefillingcurves