GIPSy updates the methodology of the previously published software, PIPS [ 30], which predicts putative PAIs by searching for regions larger than 6 kb that show genomic signature deviations (i.e., deviations in G+C content or codon usage), transposase genes, virulence factors, and flanking tRNAs.
PIPS identifies PAIs according to their main feature: genomic signature deviations, that is, G + C content and codon usage deviations; presence of virulence factors, transposase genes and flanking tRNAs genes; and absence in nonpathogenic organism from the same genus or related species.
In the endosperm of flowering plants, a ratio of two maternal and one paternal copies of the genome are optimal for development, probably because of genomic imprinting; deviations from this ratio are sometimes tolerated, but often result in disturbances in seed formation (Vinkenoog et al., 2003, Spielmann et al., 2003; Talent, 2009).
A suboptimal alignment was defined as any alignment which exceeded 3 standard deviations of the mean pairwise genomic divergence (window size 2 kb, slide 100 bp).
As for genomic imprinting effects, deviations from optimal phenotypes are expected to manifest primarily as deviations in health, such that particular alleles increase the health of one sex but decrease health of the other, or decrease the health of both.
AFLPs produced may be immediately comparable to those produced by other genomes, revealing deviations in otherwise conserved sequence, thus informing of structural-genomic variation.
Error bars show standard deviations over genomic regions.
Deviations from genomic GC content and codon usage have been used to infer potential gene transfers across bacteria [ 42, 43].
Customized Perl scripts were used to determine GC percentage of all predicted protein-coding genes on the strain SZ chromosome and pSZ77 with standard deviations from genomic averages computed in R (http://www.r-project.org/).org/
Although the dominance variance was significant for some traits, inclusion of dominance deviations in genomic prediction did not increase the accuracy of prediction of the genetic value of individuals and hence the prediction of their phenotypic values.
