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MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species

Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology...

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Detalles Bibliográficos
Autores principales: Baek, Jeong-Ho, Kim, Junah, Kim, Chang-Kug, Sohn, Seong-Han, Choi, Dongsu, Ratnaparkhe, Milind B., Kim, Do-Wan, Lee, Tae-Ho
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Libertas Academica 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003123/
https://www.ncbi.nlm.nih.gov/pubmed/27594782
http://dx.doi.org/10.4137/EBO.S40009
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author Baek, Jeong-Ho
Kim, Junah
Kim, Chang-Kug
Sohn, Seong-Han
Choi, Dongsu
Ratnaparkhe, Milind B.
Kim, Do-Wan
Lee, Tae-Ho
author_facet Baek, Jeong-Ho
Kim, Junah
Kim, Chang-Kug
Sohn, Seong-Han
Choi, Dongsu
Ratnaparkhe, Milind B.
Kim, Do-Wan
Lee, Tae-Ho
author_sort Baek, Jeong-Ho
collection PubMed
description Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies.
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spelling pubmed-50031232016-09-02 MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species Baek, Jeong-Ho Kim, Junah Kim, Chang-Kug Sohn, Seong-Han Choi, Dongsu Ratnaparkhe, Milind B. Kim, Do-Wan Lee, Tae-Ho Evol Bioinform Online Original Research Information on multiple synteny between plants and/or within a plant is key information to understand genome evolution. In addition, visualization of multiple synteny is helpful in interpreting evolution. So far, some web applications have been developed to determine and visualize multiple homology regions at once. However, the applications are not fully convenient for biologists because some of them do not include the function of synteny determination but visualize the multiple synteny plots by allowing users to upload their synteny data by determining the synteny based only on BLAST similarity information, with some algorithms not designed for synteny determination. Here, we introduce a web application that determines and visualizes multiple synteny from two types of files, simplified browser extensible data and protein sequence file by MCScanX algorithm, which have been used in many synteny studies. Libertas Academica 2016-08-28 /pmc/articles/PMC5003123/ /pubmed/27594782 http://dx.doi.org/10.4137/EBO.S40009 Text en © 2016 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License.
spellingShingle Original Research
Baek, Jeong-Ho
Kim, Junah
Kim, Chang-Kug
Sohn, Seong-Han
Choi, Dongsu
Ratnaparkhe, Milind B.
Kim, Do-Wan
Lee, Tae-Ho
MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title_full MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title_fullStr MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title_full_unstemmed MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title_short MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User’s Sequence of Interest Compared to Public Plant Species
title_sort multisyn: a webtool for multiple synteny detection and visualization of user’s sequence of interest compared to public plant species
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003123/
https://www.ncbi.nlm.nih.gov/pubmed/27594782
http://dx.doi.org/10.4137/EBO.S40009
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