digIS: automated pipeline for detecting distant, novel insertion sequence elements in prokaryotes

Insertion sequences (ISs) are short DNA elements (typically less than 5 kb) and represent the simplest transposable elements. They are widespread in prokaryotes and may occur in high numbers in their genomes. ISs play important role in prokaryotic genome structure and evolution, for example, they can cause large rearrangements in the host genome or gene inactivation. Current ISs annotation tools depend either on existing genome annotations or databases of known IS elements and lack generalization capability resulting in an inability to detect novel IS elements or distant members of individual IS families. Here we introduce a novel approach which tackles these shortcomings based on manually curated pHMMs.