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Bioinformatics Advance Access originally published online on January 10, 2006
Bioinformatics 2006 22(6):676-684; 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

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 4,5

1Department of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia
2INRIA Rocquencourt France
3University of California Berkeley, USA
4State Research Center GosNIIGenetika Moscow, Russia
5Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia

*To whom correspondence should be addressed.

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 Drosophila pseudoobscura. Tandems with period three and its multiples were found in coding segments, whereas FTRs with periods multiple of six 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: TandemSWAN web page, stand-alone version and documentation can be found at http://bioinform.genetika.ru/projects/swan/www/

Contacts: valeyo{at}imb.ac.ru

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on October 14, 2005; revised on December 22, 2005; accepted on December 28, 2005

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