hATsurface

hATsurface is a computational tool designed for the analysis of transposon insertion sites. Specifically, it focuses on the Helentransposase family (hAT) of transposons, which are widespread in eukaryotic genomes. The primary function of hATsurface is to identify and map the locations where these mobile genetic elements have inserted themselves within a DNA sequence. This is crucial for understanding the dynamics of transposon activity and its impact on genome evolution, gene regulation, and the potential for insertional mutagenesis.

The tool utilizes sequence alignment algorithms to compare a given genome sequence against known hAT transposon sequences. By identifying regions that show homology to these transposons, hATsurface can pinpoint potential insertion sites. Furthermore, it can often infer the orientation of the transposon and, in some cases, identify flanking host DNA sequences. This flanking sequence information is vital for validating insertions and for studying the process of transposition.

hATsurface is typically used in the context of next-generation sequencing data, such as whole-genome sequencing or ChIP-sequencing experiments where transposon activity is being investigated. Its output can be integrated with other bioinformatics pipelines to provide a comprehensive view of transposon landscape within an organism. Researchers employ hATsurface to study population genetics, investigate the role of transposons in disease, and explore their contribution to genome diversification.