Inter-dinucleotide distances in the human genome: an analysis of the whole-genome and protein-coding distributions

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doi doi:10.2390/biecoll-jib-2011-172
submission July 08, 2011
published September 15, 2011
NCBI PubMed PubMed ID 21926435

Carlos A.C. Bastos, Vera Afreixo, Armando J. Pinho, Sara P. Garcia, João M.O.S. Rodrigues and Paulo J.S.G. Ferreira

Correspondence should be addressed to:
Carlos Bastos
Signal Processing Lab, IEETA, University of Aveiro, 3810-193 Aveiro, Portugal
tp.au@nullsotsabc


Abstract

We study the inter-dinucleotide distance distributions in the human genome, both in the whole-genome and protein-coding regions. The inter-dinucleotide distance is defined as the distance to the next occurrence of the same dinucleotide. We consider the 16 sequences of inter-dinucleotide distances and two reading frames. Our results show a period-3 oscillation in the protein-coding inter-dinucleotide distance distributions that is absent from the whole-genome distributions. We also compare the distance distribution of each dinucleotide to a reference distribution, that of a random sequence generated with the same dinucleotide abundances, revealing the CG dinucleotide as the one with the highest cumulative relative error for the first 60 distances. Moreover, the distance distribution of each dinucleotide is compared to the distance distribution of all other dinucleotides using the Kullback-Leibler divergence. We find that the distance distribution of a dinucleotide and that of its reversed complement are very similar, hence, the divergence between them is very small. This is an interesting finding that may give evidence of a stronger parity rule than Chargaff’s second parity rule.

Reference

Carlos A.C. Bastos, Vera Afreixo, Armando J. Pinho, Sara P. Garcia, João M.O.S. Rodrigues and Paulo J.S.G. Ferreira. Inter-dinucleotide distances in the human genome: an analysis of the whole-genome and protein-coding distributions. Journal of Integrative Bioinformatics, 8(3):172, 2011. Online Journal: http://journal.imbio.de/index.php?paper_id=172
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