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Abstract
AbstractA plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could be a hint that the DNA sequence of P. falciparum has undergone certain rare mutational events.
Highlights
The DNA sequence contains all the information essential for the survival and growth of any organism [1]
The auto-correlation plot for A,T,G or C of almost any organism shows a distinct characteristic, namely that the magnitude of the auto-correlation for k = 0 is higher than that for other values of k. This feature can be linked to the presence of base 3 periodicity in genomes [8]. Though this feature is present in the plots of both CG (k) and CA (k) for P. falciparum, the plot of CA (k) has some distinct features which are probably unique in nature
Though it is known that the correlation strength at k = 0 is higher than that at other values of k, the reason for the presence of this property in almost all DNA sequences is not yet understood
Summary
The DNA sequence contains all the information essential for the survival and growth of any organism [1]. Though spontaneous mutations would have produced a random DNA sequence, induced mutations lead to certain non-random features. More non-random features are incorporated in the DNA sequence by the process of natural selection (fitness) since any random sequence of nucleotides will not be able to successfully survive and replicate in given environmental conditions. In [6], it was shown that the correlation pattern of various organisms carry a characteristic signature which can be used to construct phylogenetic trees of various eukaryotes This is an important contribution since unlike the other phylogenetic methods which are based on sequence alignment, a correlation based method is both much more simple and independent of the length of the DNA sequence. It was shown that a correlation based method is better than the conventional methods for identifying bacterial origins of replication, but it can predict the origin of replication in certain higher organisms
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