Primary Studies Of Quasi-period Patterns In Alu Repeats

This paper belongs to the category of bioinformatics. Up to now, as to human genome, only the DNA coding regions (genes) are well understood, which merely account for 3% of the whole genome. However, correlative research of this part has created about 10 Nobel Prize winners, the biological information covered in the 97% noncoding region is considerable, so searching coding feature, information regulation and expression rule are hotspots in the long future.It is important to stress that a lot of repeat interspersed sequences exist in the genome of most eukaryote. Alu repeats belong to the short interspersed elements. Their percentage in human DNA genome is about 5-6%. The latest researches indicated that Alu repeats are probably related with gene regulation network and regulates the interspersed elements in cooperating expression. As we know, that DNA uses the triple coding method to determine the amino acid sequences of proteins, so the main problem is whether Alu repeats have a coding method like triple coding or not?In this paper we attempt to find the possible coding patterns of Alu repeats with the quasi-period method. We compare the results with those of exon and intron sequences and find Alu repeats maybe use octamers as coding pattern. This supports the viewpoint that Alu repeats may participate in the compression regulating.To study more deeply the quasi-period pattern of Alu repeats, we calculated the quasi-period of the left and right monomers of Alu repeats of different families and found that the right monomers of all families show significant quasi-period 8 in their sequences while the left monomers show quasi-periods 5 or 8. We also find that the quasi-period 5 in the left monomers tends to evolve into quasi-period 8. These results indicate that there have conserved quasi-period 8 in Alu repeats, so Alu repeats may have a certain or some functions.As to Alu repeats of different families and their left and right arms, we take statistics to find the probability that 4 kinds of bases appear at each periodic site respectively and we have not found special rule. This is consistent with the experience obtained by statistical property analysis of coding region, which shows that the usage frequency of the codons in DNAs isn't a uniform distribution. However we find it is same in Alu repeats of different families and their left and right arms that the frequency of occurrence of the base G is highest, in the next place are the base A and C, the least is T.