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Algorithms 2009, 2(1), 448-469; doi:10.3390/a2010448

Structural Fingerprints of Transcription Factor Binding Site Regions

1,2,* , 1
1 Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK 2 Department of Information Studies, University of Sheffield, Sheffield, S1 4DP, UK
* Author to whom correspondence should be addressed.
Received: 4 December 2008 / Revised: 2 February 2009 / Accepted: 5 March 2009 / Published: 10 March 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
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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 spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.
Keywords: DNA structure; sequence-dependent structure; transcription factor binding site; Fourier transform; structural fingerprint DNA structure; sequence-dependent structure; transcription factor binding site; Fourier transform; structural fingerprint
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Gardiner, E.J.J.; Hunter, C.A.; Willett, P. Structural Fingerprints of Transcription Factor Binding Site Regions. Algorithms 2009, 2, 448-469.

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