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Bioinformatics Vol. 18 no. 9 2002
Pages 1153-1161
© 2002 Oxford University Press

Genome structures embossed by oligonucleotide-stickiness

Koichi Nishigaki 1,* and Ayumu Saito 1

1 Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Saitama, Saitama 338-8570, Japan

Received on October 29, 2001 ; revised on March 27, 2002 ; accepted on April 16, 2002

Motivation: An unmanageably large amount of data on genome sequences is accumulating, prompting researchers to develop new methods to analyze them. We have devised a novel method designated oligostickiness, a measure roughly proportional to the binding affinity of an oligonucleotide to a DNA of interest, in order to analyze genome sequences as a whole.

Results: Fifteen representative genomes such as Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, H. sapiens and others were analyzed by this method using more than 50 probe dodecanucleotides, offering the following findings: (i) Genome sequences can be specifically featured by way of oligostickiness maps. (ii) Oligostickiness analysis, which is similar to but more informative than (G + C) content or repetitive sequence analysis, can reveal intra-genomic structures such as mosaic structures (E. coli and B. subtilis) and highly sticky/non-sticky regions of biological meanings. (iii) Some probe oligonucleotides such as dC12 and dT12 can be used for classifying genomes, clearly discriminating prokaryotes and eukaryotes. (iv) Based on global oligostickiness, which is the average value of the local oligostickinesses, the features of a genome could be visualized in spider web mode. The pattern of a spider web as well as a set of oligostickiness maps is highly characteristic to each genome or chromosome. Thus, we called it as chromosome texture, leading to a finding that all the chromosomes contained in a cell, so far investigated, have a common texture.

Availability: Oligostickinesses maps used in this work are available at http://gp.fms.saitama-u.ac.jp/

Contact: koichi{at}fms.saitama-u.ac.jp

* To whom correspondence should be addressed.


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