Bioinformatics study of the mangrove actin genes

International Conference on Computing and Applied Informatics 2016

物理学;计算机科学

Basyuni, M.^1 ; Wasilah, M.^1 ; Sumardi^2

Department of Forestry, Faculty of Forestry, University of Sumatera Utara, J1.Tri Dharma Ujung No. 1, Medan, North Sumatera

20155, Indonesia^1

Faculty of Pharmacy, Tjut Nyak Dhien University, Jl. Rasmi No. 28, Medan

20123, Indonesia^2

关键词: Bioinformatics methods;    Chain structure;    Phylogenetic trees;    Physical and chemical properties;    Secondary structures;    Structural information;    Subcellular localizations;    Transit peptides;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/801/1/012013/pdf
DOI  :  10.1088/1742-6596/801/1/012013

学科分类：计算机科学（综合）

来源: IOP

【 摘 要 】

This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.