A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups

A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups

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We developed simulation tool for influenza virus variation (SimFluVar), an analytics software for calculating genomic variation among members of the influenza virus group. This study is related to computational evolutionary biology and evolutionary bioinformatics. SimFluVar is an analytical tool tha...

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Main Authors: Insung Ahn, Jin-Hwa Jang, Ha-Yeon Kim, Ji-Hae Lee, Hyeon Seok Son
Format: Article
Language:English
Published: SAGE Publishing 2015-01-01
Series:Evolutionary Bioinformatics
Online Access:https://doi.org/10.4137/EBO.S28844
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spelling doaj-4cc662eb46f24c12a76e96a0d3d797302020-11-25T03:15:47ZengSAGE PublishingEvolutionary Bioinformatics1176-93432015-01-011110.4137/EBO.S28844A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different GroupsInsung Ahn0Jin-Hwa Jang1Ha-Yeon Kim2Ji-Hae Lee3Hyeon Seok Son4Biomedical Prediction Technology Laboratory, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Republic of Korea.Laboratory of Computational Biology and Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Gwanak-gu, Seoul, Republic of Korea.Laboratory of Computational Biology and Bioinformatics, Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Gwanak-gu, Seoul, Republic of Korea.Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Gwanak-gu, Seoul, Republic of Korea.Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Gwanak-gu, Seoul, Republic of Korea.We developed simulation tool for influenza virus variation (SimFluVar), an analytics software for calculating genomic variation among members of the influenza virus group. This study is related to computational evolutionary biology and evolutionary bioinformatics. SimFluVar is an analytical tool that can be used to calculate codon substitution patterns of viral genes. Designed to compare a large number of nucleotide sequences, SimFluVar provides precise patterns of codon variations between two viral groups, especially for the influenza virus. SimFluVar also provides useful functions, such as editing and visualization of the result matrix. This new tool can be used to analyze codon variation patterns over time as well as to analyze the genomic differences between viruses obtained from different geographical locations. SimFluVar is developed in C++, and Java RCP is used as a distribution package. SimFluVar, including the associated documentation, manuals, and examples, is publicly available at http://lcbb.snu.ac.kr/simfluvar .https://doi.org/10.4137/EBO.S28844
collection DOAJ
language English
format Article
sources DOAJ
author Insung Ahn
Jin-Hwa Jang
Ha-Yeon Kim
Ji-Hae Lee
Hyeon Seok Son
spellingShingle Insung Ahn
Jin-Hwa Jang
Ha-Yeon Kim
Ji-Hae Lee
Hyeon Seok Son
A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
Evolutionary Bioinformatics
author_facet Insung Ahn
Jin-Hwa Jang
Ha-Yeon Kim
Ji-Hae Lee
Hyeon Seok Son
author_sort Insung Ahn
title A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
title_short A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
title_full A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
title_fullStr A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
title_full_unstemmed A Visualization Tool for Calculating the Genetic Substitution Patterns between Two Different Groups
title_sort visualization tool for calculating the genetic substitution patterns between two different groups
publisher SAGE Publishing
series Evolutionary Bioinformatics
issn 1176-9343
publishDate 2015-01-01
description We developed simulation tool for influenza virus variation (SimFluVar), an analytics software for calculating genomic variation among members of the influenza virus group. This study is related to computational evolutionary biology and evolutionary bioinformatics. SimFluVar is an analytical tool that can be used to calculate codon substitution patterns of viral genes. Designed to compare a large number of nucleotide sequences, SimFluVar provides precise patterns of codon variations between two viral groups, especially for the influenza virus. SimFluVar also provides useful functions, such as editing and visualization of the result matrix. This new tool can be used to analyze codon variation patterns over time as well as to analyze the genomic differences between viruses obtained from different geographical locations. SimFluVar is developed in C++, and Java RCP is used as a distribution package. SimFluVar, including the associated documentation, manuals, and examples, is publicly available at http://lcbb.snu.ac.kr/simfluvar .
url https://doi.org/10.4137/EBO.S28844
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