TR-IIS-04-019    PDF format

Abstract

Motivation: It has been of great interest to know whether some simple nucleotide-level patterns or permutation structures can give rise to genome-wide general properties. In this study, we wish to find such patterns or structures. For this purpose, we develop a representation method different from those used to detect long range correlations (LRCs) in genomes. Specifically, we propose a set of crystalline-like walking spaces in which DNA sequences can be coded into a set of 3D curves by following a set of walking rules.
Results: Our representation method reveals that genomic DNA sequences in both prokaryotes and eukaryotes have linear trends and discernable orientations in the walking spaces. Some palindrome-like sequences are then found to have the trends and orientations similar to those found in genomic DNA sequences. After a series of verifications and simulations, we speculate that these patterns may be derived from a very old ancestral genome and some of the patterns might still possess certain functions in present-day genomes. These patterns may explain the existence of LRCs in genomes and why Chargaff's second parity rule holds approximately in many genomic regions.