AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

by Andrew J. Page, Sarah Bastkowski, Muhammad Yasir, A. Keith Turner, Thanh Le Viet, George M. Savva, Mark A. Webber, Ian G. Charles Bacteria need to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon directed insertion-site sequencing (TraDIS) is a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this ap proach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to differe nt conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction. To address this analysis need, we have developed ‘AlbaTraDIS’; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transpo son insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list ...
Source: PLoS Computational Biology - Category: Biology Authors: Source Type: research