geneCo: a visualized comparative genomic method to analyze multiple genome structures.

Abstract

In comparative and evolutionary genomics, a detailed comparison of common features between organisms is essential to evaluate genetic distance. However, identifying differences in matched and mismatched genes among multiple genomes is difficult using current comparative genomic approaches due to complicated methodologies or the generation of meager information from obtained results. This study describes a visualized software tool, geneCo (gene Comparison), for comparing genome structure and gene arrangements between various organisms. User data are aligned, gene information is recognized, and genome structures are compared based on user-defined GenBank files. Information regarding inversion, gain, loss, duplication and gene rearrangement among multiple organisms being compared is provided by geneCo, which uses a web-based interface that users can easily access without any need to consider the computational environment. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/geneCo. The main module of geneCo is implemented by Python and the web-based user interface is built by PHP, HTML and CSS to support all browsers. Supplementary data are available at Bioinformatics online.