title: PanGeT: Pan-genomics tool.
abstract: 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.
authors.affiliation: Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Iyyappan
authors.initials: I
authors.lastname: Yuvaraj
authors.affiliation: Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India; Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai 625021, India.
authors.forename: Jayavel
authors.initials: J
authors.lastname: Sridhar
authors.affiliation: Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Daliah
authors.initials: D
authors.lastname: Michael
authors.affiliation: Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India. Electronic address: sekar@cds.iisc.ac.in.
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics / Q000706:statistics & numerical data*; D009161:Mycobacterium / Q000145:classification / Q000235:genetics; D020543:Proteome / Q000235:genetics; D019779:Salmonella enterica / Q000145:classification / Q000235:genetics; D012984:Software; D013045:Species Specificity
chemical_list: D020543:Proteome
keywords: CDS; Core genes; Dispensable genes; Genome; Pan-genome; Proteome; Species; Unique genes