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We first focused on large genomic segments that differ between S. paratyphi C RKS4594 and S. choleraesuis SC-B67, as they are supposed to be laterally acquired and contain large numbers of genes that may have facilitated the pathogenic divergence process.
We identified 38 OP-type clusters of segments that differ in their compositional spectrum (CS) organization.
The Joinpoint Program uses permutation tests to find a best fit of regression model with the smallest number of "joinpoints" which are distinct linear segments that differ statistically in their slopes.
Similarly, rod and cone photoreceptors contain highly elaborate ciliary outer segments that differ in morphology, and that localize molecules required for phototransduction (Berbari et al., 2009; Yildiz and Khanna, 2012).
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For each such GC range, we identified large groups of segments that differed in their CS organization (referred to as OP groups), and compared the genes residing in segments of the same OP group; 13 of the 38 OP groups showed significant enrichment in genes connected to specific gene-ontology (GO) terms.
A top-hat is a residual filter that preserves those features in an image that can fit within the structuring element and removes those that cannot; in other words, the top-hat transform is used to segment objects that differ in brightness from the surrounding background in images with uneven background intensity.
The diploidization process, involving non-homologous recombination events together with deletions and pseudogenizations of genes, generates duplicated chromosomes that differ in large segments, but still exhibit paralogous regions.
This possibility needs to be explored in much larger series of lesions that differ in stage (size) and segment of origin.
We observed that V. cholerae strains encode a diversity of Tap-1 proteins that differ in their N- and C-terminal segments.
The 3rd segment that differs between the two studies (D vs. B″) is AINRKIDRINKIASAGKGVGGFSGAGRSASPEPIYAQVAKKVSAKIDQLNEATS.
Most importantly, the segment that differs between the fertile and non-fertile lines is only ~1.4 Mb and contains only 174 known protein coding genes.
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