Synteny Portal: a web-based application portal for synteny block analysis

Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny block...

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Main Authors:	Lee, Jongin, Hong, Woon-young, Cho, Minah, Sim, Mikang, Lee, Daehwan, Ko, Younhee, Kim, Jaebum
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987893/

id	pubmed-4987893
recordtype	oai_dc
spelling	pubmed-49878932016-08-22 Synteny Portal: a web-based application portal for synteny block analysis Lee, Jongin Hong, Woon-young Cho, Minah Sim, Mikang Lee, Daehwan Ko, Younhee Kim, Jaebum Web Server issue Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal. Oxford University Press 2016-07-08 2016-05-06 /pmc/articles/PMC4987893/ /pubmed/27154270 http://dx.doi.org/10.1093/nar/gkw310 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), 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
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lee, Jongin Hong, Woon-young Cho, Minah Sim, Mikang Lee, Daehwan Ko, Younhee Kim, Jaebum
spellingShingle	Lee, Jongin Hong, Woon-young Cho, Minah Sim, Mikang Lee, Daehwan Ko, Younhee Kim, Jaebum Synteny Portal: a web-based application portal for synteny block analysis
author_facet	Lee, Jongin Hong, Woon-young Cho, Minah Sim, Mikang Lee, Daehwan Ko, Younhee Kim, Jaebum
author_sort	Lee, Jongin
title	Synteny Portal: a web-based application portal for synteny block analysis
title_short	Synteny Portal: a web-based application portal for synteny block analysis
title_full	Synteny Portal: a web-based application portal for synteny block analysis
title_fullStr	Synteny Portal: a web-based application portal for synteny block analysis
title_full_unstemmed	Synteny Portal: a web-based application portal for synteny block analysis
title_sort	synteny portal: a web-based application portal for synteny block analysis
description	Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987893/
_version_	1613628883535396864

Synteny Portal: a web-based application portal for synteny block analysis

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