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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Libertas Academica
2016
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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. |
format | Online Article Text |
id | pubmed-5003123 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
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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