Applications of recursive segmentation to the analysis of DNA sequences

Li, W. T., Bernaola-Galvan, P., Haghighi, F., Grosse, I. (July 2002) Applications of recursive segmentation to the analysis of DNA sequences. Computers & Chemistry, 26 (5). pp. 491-510. ISSN 0097-8485

URL: http://www.ncbi.nlm.nih.gov/pubmed/12144178
DOI: 10.1016/S0097-8485(02)00010-4

Abstract

Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G + C)/weak(A + T) sequence, to a binary sequence indicating the presence or absence of the dinucleotide CpG, or to a sequence indicating both the base and the codon position information. We apply various conversion schemes in order to address the following five DNA sequence analysis problems: isochore mapping, CpG island detection, locating the origin and terminus of replication in bacterial genomes, finding complex repeats in telomere sequences, and delineating coding and noncoding regions. We find that the recursive segmentation procedure can successfully detect isochore borders, CpG islands, and the origin and terminus of replication, but it needs improvement for detecting complex repeats as well as borders between coding and noncoding regions.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: July 2002
Date Deposited: 08 Jan 2014 17:45
Last Modified: 08 Jan 2014 17:45
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28734

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