Large-scale Asymmetries in the DNA of E. coli
نویسنده
چکیده
Compositional asymmetries in circular bacterial chromosomes exist on a large-scale. Using a sliding window to take the average concentration of nucleotides across a length equal to one-half of the chromosome (~2.3 million characters), it is possible to to split the E. Coli genome into two distinct region: one with a bias in C concentration and the other with a bias in G concentration. This genome wide asymmetry is known as GC skew and is due to the two-stranded structure of the chromosome. What drives this difference in composition? How is it actualized in a given sequence? A generic method is presented using regular expressions and mutual information to find embedded structure in these two regions. This technique should be able to identify the still debated explanation of third codon position bias responsible for GC skew, but might also identify other possible explanations should they exist.
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