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Bioinformatics Advance Access published online on January 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk032
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 14, 2005
Revised December 22, 2005
Accepted December 28, 2005

Article

Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression

Valentina Boeva 1 *, Mireille Regnier 2, Dmitri Papatsenko 3, and Vsevolod Makeev 4

1 Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
2 INRIA Rocquencourt, France
3 University of California, Berkeley, USA
4 State Research Center GosNIIGenetika, Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

* To whom correspondence should be addressed.
Valentina Boeva, E-mail: valeyo{at}imb.ac.ru


  Abstract

Motivation: Genomic sequences are highly redundant and contain many types of repetitive DNA. Fuzzy tandem repeats (FTRs) are of particular interest. They are found in regulatory regions of eukaryotic genes and are reported to interact with transcription factors. However, accurate assessment of FTR occurrences in different genome segments requires specific algorithm for efficient FTR identification and classification.

Results: We have obtained formulas for P-values of FTR occurrence and developed an FTR identification algorithm implemented in TandemSWAN software. Using TandemSWAN we compared the structure and the occurrence of FTRs with short period length (up to 24 bp) in coding and non-coding regions including UTRs, heterochromatic, intergenic, and enhancer sequences of Drosophila melanogaster and D. pseudoobscura. Tandems with period 3 and its multiples were found in coding segments, whereas FTRs with periods multiple of 6 are overrepresented in all non-coding segment. Periods equal to 5-7 and 11-14 were characteristic of the enhancer regions and other non-coding regions close to genes.

Availability: Availability: TandemSWAN web page, stand-alone version, and documentation can be found at http://bioinform.genetika.ru/projects/swan/www/.

Associate Editor: Steven Salzberg
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