Abstract
BackgroundThe dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the causes and the functional significance of this phenomenon could be illuminated by determining if it persists on smaller scales. The profile is computed from the base step "odds ratios" that compare dinucleotide frequencies to those expected under the assumption of stochastic equilibrium (thorough shuffling). Analysis is carried out on 22 sequences, representing 19 species and comprised of about 53 million bases all together, to assess stability of the signature in windows ranging in size from 50 kilobases down to 125 bases.ResultsDinucleotide relative abundance distance from the global signature is computed locally for all non-overlapping windows on each sequence. These distances are log-normally distributed with nearly constant variance and with means that tend to zero slower than reciprocal square root of window size. The mean distance within genomes is larger for protist, plant, and human chromosomes, and smaller for archaea, bacteria, and yeast, for any window size.ConclusionsThe imprint of the global signature is locally pervasive on all scales considered in the sequences (either genomes or chromosomes) that were scanned.
Highlights
The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome
"genomic signature" that reflects a "total net response to selective pressure [6]." Yet the 50 kb window spans the complete genome of bacteriophage lambda and it would not be surprising to discover local instability in the profile seen through smaller windows
Except for the Borrelia burgdorferi sequence, the mean scaled deltadistance is increasing in window size for every sequence
Summary
The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the causes and the functional significance of this phenomenon could be illuminated by determining if it persists on smaller scales. Bacterial genomes commonly exhibit an approximate balance between purine (A+G) and pyrimidine (C+T) fractions, and between amino (A+C) and keto (G+T) fractions, when the whole leading strand is examined These fractions fluctuate from their global averages almost as dramatically as the strong (C+G) and weak (A+T) fractions that do not show global balance.
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