PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions and in the organization of chromosomes in both eukaryotes and prokaryotes. Local differences in DNA sequence periodicity have been linked to differences in gene expression in some organisms. Despite the significance of these periodic patterns, there are virtually no publicly accessible tools for their analysis.
genome periodic spacing chromosome gene expression software dna structure nucleoid chromatin a-tracts