GenePlots: Large-Scale Gene Structures Visualization and Comparison Based on GenBank CDS Annotations

Title:GenePlots: Large-Scale Gene Structures Visualization and Comparison Based on GenBank CDS Annotations

Volume: 10 Issue: 4

Author(s): Haijun Liu, Keping Chen, Haifeng Shi, Keming Zhu and Xiaoyong Liu

Affiliation:

Keywords: Exon and intron, intron phase, GenBank CDS annotation, GenePlots, gene structure visualization, software.

Abstract: Drawing and comparing structures of homologous genes is an important way to study the gene evolution. In recent years, several programs and web tools have been proposed to draw gene structures according to genome sequences or GFF (General Feature Format) gene data. It is unfitted for them to draw a large number of gene structures due to time-consuming preparation of input data. The visualization tools for comparing the structures of hundreds or even thousands of genes are particularly lacking. We developed GenePlots, a comparative and interactive viewer for large scale gene structures based on CDS annotations in GenBank. With CDS annotations formatted like FASTA, GenePlots can draw all exon-intron structures for numerous genes in a unified scale. The most important assets of GenePlots are: (i) using GenBank CDS annotations as input data; (ii) the capability for analyzing thousands of genes simultaneously; (iii) the exhibition of intron phase; (iv) the flexibility allowing users to change the resulting diagram. GenePlots provides a simple and high efficient way to produce a large number of gene structures for large-scale genes comparison.

Cite this article as:

Liu Haijun, Chen Keping, Shi Haifeng, Zhu Keming and Liu Xiaoyong, GenePlots: Large-Scale Gene Structures Visualization and Comparison Based on GenBank CDS Annotations, Current Bioinformatics 2015; 10 (4) . https://dx.doi.org/10.2174/157489361004150922152120