Skip Navigation


Bioinformatics Advance Access originally published online on January 10, 2006
Bioinformatics 2006 22(6):676-684; doi:10.1093/bioinformatics/btk032
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/6/676    most recent
btk032v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Boeva, V.
Right arrow Articles by Makeev, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Boeva, V.
Right arrow Articles by Makeev, V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
S. B. Mudunuri and H. A. Nagarajaram
IMEx: Imperfect Microsatellite Extractor
Bioinformatics, May 15, 2007; 23(10): 1181 - 1187.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Archak, E. Meduri, P. S. Kumar, and J. Nagaraju
InSatDb: a microsatellite database of fully sequenced insect genomes
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D36 - D39.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.