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The nucleotide genomic signal (NuGS) methodology is based on the conversion of symbolic nucleotide sequences into genomic signals, allowing the use of signal processing methods to investigate genetic information. The approach is adequate for both the large scale analysis of genomes and for the monitoring of local variations in genomic sequences, such as those caused by pathogen variability or by genomic inserts. The inserts can comprise retro-viruses, individual genes, or non-coding segments. Even when the inserts are not fully active viruses, they can still retain a significant pathogenicity when encoding viral enzymes that can facilitate the dissemination of some viruses, generating an increased susceptibility to the contamination with these pathogens. Inserts occur usually in complementary pairs, with the tendency to restore the original regularities of the host genome. The paper illustrates the NuGS methodology for two typical cases: the insert of the SPBc2 bacillusphage complete genome in the genome of Bacillus subtilis and the inserts of genes from the PE-PGRS family in the genome of Mycobacterium tuberculosis.