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. <br><br>The directories: "Data", "Results", "Scripts", and "synteny_block_search" are used for psi-blast search and visualization of the results.<br><br>Synteny block search requires protein database and gff files available from Zenodo repository:<br>Gammaproteobacteria protein dataset: <br>doi 10.5281/zenodo.5880327 <br><br>Alphaproteobacteria protein dataset: <br>doi 10.5281/zenodo.5885703 <br><br>Betaproteobacteria protein dataset: <br>doi 10.5281/zenodo.5885688 <br><br>"attS_sequencing" directory contains README.txt which contains all commands used for attS amplicon sequencing.<br>"resequencing" directory contains README.txt and illumina reads assemblies of single gene knockout mutants as well as parent strain BHY606.<br><br><br><br>