Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis

Biochem Biophys Res Commun. 2003 Nov 7;311(1):215-22. doi: 10.1016/j.bbrc.2003.09.198.

Abstract

Incorporated with the Z curve method, the technique of wavelet multiresolution (also known as multiscale) analysis has been proposed to identify the boundaries of isochores in the human genome. The human MHC sequence and the longest contigs of human chromosomes 21 and 22 are used as examples. The boundary between the isochores of Class III and Class II in the MHC sequence has been detected and found to be situated at the position 2,490,368bp. This result is in good agreement with the experimental evidence. An isochore with a length of about 7Mb in chromosome 21 has been identified and found to be gene- and Alu-poor. We have also found that the G+C content of chromosome 21 is more homogeneous than that of chromosome 22. Compared with the window-based methods, the present method has the highest resolution for identifying the boundaries of isochores, even at a scale of single base. Compared with the entropic segmentation method, the present method has the merits of more intuitiveness and less calculations. The important conclusion drawn in this study is that the segmentation points, at which the G+C content undergoes relatively dramatic changes, do exist in the human genome. These 'singularity' points may be considered to be candidates of isochore boundaries in the human genome. The method presented is a general one and can be used to analyze any other genomes.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms
  • Base Sequence
  • Chromosomes, Human, Pair 21 / genetics*
  • Chromosomes, Human, Pair 22 / genetics*
  • GC Rich Sequence / genetics
  • Genome, Human*
  • Humans
  • Isochores / genetics*
  • Major Histocompatibility Complex / genetics*
  • Molecular Sequence Data
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Signal Processing, Computer-Assisted*

Substances

  • Isochores