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mySyntenyPortal: an application package to construct websites for synteny block analysis

BACKGROUND: Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require...

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Autores principales: Lee, Jongin, Lee, Daehwan, Sim, Mikang, Kwon, Daehong, Kim, Juyeon, Ko, Younhee, Kim, Jaebum
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989462/
https://www.ncbi.nlm.nih.gov/pubmed/29871588
http://dx.doi.org/10.1186/s12859-018-2219-x
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author Lee, Jongin
Lee, Daehwan
Sim, Mikang
Kwon, Daehong
Kim, Juyeon
Ko, Younhee
Kim, Jaebum
author_facet Lee, Jongin
Lee, Daehwan
Sim, Mikang
Kwon, Daehong
Kim, Juyeon
Ko, Younhee
Kim, Jaebum
author_sort Lee, Jongin
collection PubMed
description BACKGROUND: Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. RESULTS: To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. CONCLUSIONS: mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data.
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spelling pubmed-59894622018-06-21 mySyntenyPortal: an application package to construct websites for synteny block analysis Lee, Jongin Lee, Daehwan Sim, Mikang Kwon, Daehong Kim, Juyeon Ko, Younhee Kim, Jaebum BMC Bioinformatics Software BACKGROUND: Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. RESULTS: To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. CONCLUSIONS: mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data. BioMed Central 2018-06-05 /pmc/articles/PMC5989462/ /pubmed/29871588 http://dx.doi.org/10.1186/s12859-018-2219-x Text en © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Lee, Jongin
Lee, Daehwan
Sim, Mikang
Kwon, Daehong
Kim, Juyeon
Ko, Younhee
Kim, Jaebum
mySyntenyPortal: an application package to construct websites for synteny block analysis
title mySyntenyPortal: an application package to construct websites for synteny block analysis
title_full mySyntenyPortal: an application package to construct websites for synteny block analysis
title_fullStr mySyntenyPortal: an application package to construct websites for synteny block analysis
title_full_unstemmed mySyntenyPortal: an application package to construct websites for synteny block analysis
title_short mySyntenyPortal: an application package to construct websites for synteny block analysis
title_sort mysyntenyportal: an application package to construct websites for synteny block analysis
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989462/
https://www.ncbi.nlm.nih.gov/pubmed/29871588
http://dx.doi.org/10.1186/s12859-018-2219-x
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