Analyzing Ultraconserved Elements And Splice Sites In Vertebrate Genomes

Human genome project is the first initiated vertebrate genome project. Following this, the genomes of zebra and mouse were sequenced as model organisms. Now more and more vertebrate genome sequencing tasks have been completed, such as chicken, dog, cattle, chimpanzee and fugu fish. It is an important research direction of bioinformatics to sequence vertebrate genomes and study them through the comparative genomics approach. Firstly, the incentive of this research is for better identification and characterization of human genes and their regulatory elements, especially those that are mutated in human diseases. Secondly, it is for a better understanding of the mechanisms of vertebrate genome evolution and the discovery of what makes humans unique.The conservation among vertebrate species has become an hot issue in recent years. It has been discovered that distantly related species often share long conserved stretches of DNA that do not appear to code for any protein such as the ultraconserved elements. But the function of such ultra-conserved regions remains unknown.The paper is devoted to analyze the ultraconserved elements and the splice sites in vertebrate genomes by the Z curve method. The Z curve theory, developed by Dr. Chun-Ting Zhang, provides an intuitive tool for visualizing and analyzing DNA sequences. The Z curve is a three-dimensional curve which has one-to-one correspondence to the DNA sequence.We have drawn the Z'curves of the 481 ultra-conserved elements and the human chromosomes. Also we have represented the distribution of ultraconserved elements among the human chromosomes. As to the splice sites, we analyze them through a signal search way and apply a new segmentation algorithm for DNA sequences which is based on the Z curve method.