PT  - JOURNAL ARTICLE
AU  - E.G. Mogro
AU  - N. Ambrosis
AU  - M.J. Lozano
TI  - Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
AID  - 10.1101/2020.10.16.342287
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.16.342287
4099  - http://biorxiv.org/content/early/2020/10/16/2020.10.16.342287.short
4100  - http://biorxiv.org/content/early/2020/10/16/2020.10.16.342287.full
AB  - Motivation Bacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes.Results We developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.Availability and implementation ISCompare was implemented in python3 and its source code is freely available for download at https://github.com/mauriilozano/ISCompare.Supplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.