Detection Of Isochore Boundaries In Human Genome With Double Windows Model And Wavelet Multiresolution Analysis

The mosaic organization of mammalian genomes (including human being) composed of many regions of rather homogeneous GC content was revealed by the ultracentrifugation experiments of bulk DNA in the mid-1970s by Bernardi and his coworkers. The so called isochore is many DNA fragments in the genomes, whose length is at least 200kb. The GC content within the fragments is homogenous, but the GC content of the adjacent fragments is quite different and sharply change at the boundaries. There is a strong relationship between the isochore structure of genomes and many important biological characteristics.With completion of the human genome sequencing project, it is more convenient to study its isochore structure on the sequence level. In this paper, we use the newly developed double windows sliding model, together with the theory of wavelet multiresolution analysis, to detect isochore boundaries of human DNA sequences, including Human Major Histocompatibility Complex (MHC) sequence, chromosome 21, chromosome 22, chromosome Y, and the longest contig of chromosome 21 and chromosome 22. In our work, the boundary between isochore ClassIII and isochore Class II of MHC sequence is predicted at 2,485,798 bp, which inosculates well with the experimental evidence. As a matter of fact, it represents that the window model is powerful when is effectively used.In chapterâ… , there is an introduction of the human genome project (HGP) and biological knowledge related to our research. Also, the developments and accomplishments of bioinformatics are traced.In chapterâ…¡, the theory of double window model method is elaborated. In chapterâ…¢, the theory of wavelet multiresolution analysis is introduced. The wavelet multiresolution analysis is a useful tool for studying non-stationary signal. With wavelet de-noising technique, the noising signals are filtered out and the sharp transitions are located.In chapterâ…£, the isochore structure of human genome is studied, including Human Major Histocompatibility Complex (MHC), chromosome 21, chromosome 22 chromosome Y, and the longest contig of chr21 and chr22.In chapterâ…¤, introducing some softs for gene finding, and have an overview about pathogenicity islands in Intestinal bacteria genomes.