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structural fingerprints of transcription factor binding site regions转录因子结合位点区域的结构的指纹
Algorithms 2009, 2, 448-469; doi:10.3390/a2010448
OPEN ACCESS
algorithms
ISSN 1999-4893
/journal/algorithms
Article
Structural Fingerprints of Transcription Factor Binding Site
Regions
Eleanor J. Gardiner 1, 2,*, Christopher A. Hunter 1 and Peter Willett 2
1 Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, United Kingdom
E-Mail: c.hunter@sheffield.ac.uk (C.A.H.)
2 Department of Information Studies, University of Sheffield, Sheffield, S1 4DP, United Kingdom
E-Mail: p.willett@sheffield.ac.uk (P.W.)
* Author to whom correspondence should be addressed. E-Mail: e.gardiner@sheffield.ac.uk;
Tel.: 00 44 (0)114 2222 673; Fax: 00 44 (0)114 278 0300
Received: 4 December 2008; in revised version: 2 February 2009 / Accepted: 5 March 2009 /
Published: 10 March 2009
Abstract: Fourier transforms are a powerful tool in the prediction of DNA sequence
properties, such as the presence/absence of codons. We have previously compiled a
database of the structural properties of all 32,896 unique DNA octamers. In this work we
apply Fourier techniques to the analysis of the structural properties of human chromosomes
21 and 22 and also to three sets of transcription factor binding sites within these
chromosomes. We find that, for a given structural property, the structural property power
spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their
power spectra for both Sp1 and p53 transcription factor binding sites. We use the power
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