In silico analysis of genetic diversity of begomovirus using homology modelling

Abstract

Structural bioinformatics is concerned with computational approaches to predict and analyse the spatial structure of proteins and nucleic acids. The 3D models can be obtained most easily if the 3D structure of a homologous protein is known (homology modeling, comparative modeling). Homology modeling or comparative modeling is based on the fact that a structure of a protein can be reliably modeled when its sequence is sufficiently similar to a protein sequence with known 3D structure. The Geminivirus taxonomic group of plant viruses is characterized by geminate particles and genomes consisting of single-stranded circular DNA (sscDNA) molecules of about 2-5 to 2.8 kb in size. Here, we analyzed the genetic diversity of begomovirus from different crops and weeds of different region on the basis of homology modeling. This high degree of genetic diversity suggests a recent transfer of indigenous begomovirus from wild hosts into economic important crops. © 2010 Asian Network for Scientific Information.