ExplorePipolin: reconstruction and annotation of piPolB-encoding bacterial mobile elements from draft genomes.

ABSTRACT:

Motivation

Detailed and accurate analysis of mobile genetic elements (MGEs) in bacteria is essential to deal with the current threat of multiresistant microbes. The overwhelming use of draft, contig-based genomes hinder the delineation of the genetic structure of these plastic and variable genomic stretches, as in the case of pipolins, a superfamily of MGEs that spans diverse integrative and plasmidic elements, characterized by the presence of a primer-independent DNA polymerase.

Results

ExplorePipolin is a Python-based pipeline that screens for the presence of the element and performs its reconstruction and annotation. The pipeline can be used on virtually any genome from diverse organisms and of diverse quality, obtaining the highest-scored possible structure and reconstructed out of different contigs if necessary. Then, predicted pipolin boundaries and pipolin encoded genes are subsequently annotated using a custom database, returning the standard file formats suitable for comparative genomics of this mobile element.

Availability and implementation

All code is available and can be accessed here: github.com/pipolinlab/ExplorePipolin.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

SUBMITTER: Chuprikova L 

PROVIDER: S-EPMC9710591 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature