Datasets and scripts used in 'Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria'

This directory contains data sets and scripts used in "host range of SE: a new class of mobile DNA elements nesting in Gammaproteobacteria" authored by Desmila Idola, Hiroshi Mori, Yuji Nagata, Lisa Nonaka, and Hirokazu Yano.

The directories: "Data", "Results", "Scripts", and "synteny_block_search" are used for psi-blast search and visualization of the results.

Synteny block search requires protein database and gff files available from Zenodo repository:

Gammaproteobacteria protein dataset: 

doi 10.5281/zenodo.5880327

Betaproteobacteria protein dataset:

doi 10.5281/zenodo.5885688

Alphaproteobacteria protein dataset:

doi 10.5281/zenodo.7839301

"attS_sequencing" directory contains README.txt which contains all commands used for attS amplicon sequencing.

"resequencing" directory contains README.txt and illumina reads assemblies of single gene knockout mutants as well as parent strain BHY606.