Yuvaraj Iyyappan, Sridhar Jayavel, Michael Daliah, Sekar Kanagaraj
Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India; Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 625021, India.
Gene. 2017 Feb 5;600:77-84. doi: 10.1016/j.gene.2016.11.025. Epub 2016 Nov 13.
A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines. The root of pan-genomic studies, however, is to identify the core genes, dispensable genes and strain specific genes across the genomes belonging to a clade. To this end, we have developed a tool, "PanGeT - Pan-genomics Tool" to compute the 'pan-genome' based on comparisons at the genome as well as the proteome levels. This automated tool is implemented using LaTeX libraries for effective visualization of overall pan-genome through graphical plots. Links to retrieve sequence information and functional annotations have also been provided. PanGeT can be downloaded from http://pranag.physics.iisc.ernet.in/PanGeT/ or https://github.com/PanGeTv1/PanGeT.
在泛基因组概念首次提出十年后，该领域的研究已将触角延伸至疾病发病机制、细菌进化研究和耐药性等领域。基于基因内容区分细菌的致病和非致病菌株以及鉴定病原体特异性基因对于理解它们的生理学并深入了解基因组进化机制至关重要。随后，这将有助于确定诊断靶点以及开发和选择疫苗。然而，泛基因组研究的核心是识别属于一个进化枝的基因组中的核心基因、可有可无基因和菌株特异性基因。为此，我们开发了一个工具“PanGeT - 泛基因组工具”，用于基于基因组和蛋白质组水平的比较来计算“泛基因组”。这个自动化工具使用LaTeX库实现，通过图形化绘图有效地可视化整个泛基因组。还提供了检索序列信息和功能注释的链接。PanGeT可从http://pranag.physics.iisc.ernet.in/PanGeT/ 或https://github.com/PanGeTv1/PanGeT下载。
