A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups.
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.
Biomedical Prediction Technology Laboratory, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Republic of Korea.
Insung
I
Ahn
Biomedical 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.
Jin-Hwa
JH
Jang
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.
Ha-Yeon
HY
Kim
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.
Ji-Hae
JH
Lee
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.
Hyeon Seok
HS
Son
GC pattern; codon variation; influenza A virus; simulation; transition matrix