Fig. 1
SHIP identification of putative genomic safe harbors (pGSHs). (A) Strategy overview of the eukaryotic genomic Safe Harbor Identification Program. The first step involved the design of the Safe Harbor Identification Program (SHIP), an algorithm for searching genomic safe harbors in eukaryotes from general feature data (Design); S. cerevisiae was chosen for the in vivo validation of SHIP, resulting in its genetic transformation of two overlapping BioBricks composed of a reporter gene and an auxotrophic marker (Test); followed by the analysis steps (Analysis). (B) Representative scheme of the SHIP software. As inputs, a genomic annotation (.gff3), a regulatory annotation (.gff3), and two files (.json) with the indication of genetic parts to be considered for pGSH selection. As output files, the algorithm returns a table and a graph (.png) with the distribution of intergenic distances and a file (.txt) with the list of intergenic regions and regulatory aspects. (C) Histogram with the genomic distribution of the intergenic regions between the three possible arrangements of the flanking genes. (D) Chromosome number, coordinates, neighboring genes, and size of the intergenic regions identified as pGSH. (E) Ideogram marking the identified pGSHs generated with Ideogram.js76.
