Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (9)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Parisi, V.
Right arrow Articles by Aluffi-Pentini, F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Parisi, V.
Right arrow Articles by Aluffi-Pentini, F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 14 2003
Pages 1733-1738
© 2003 Oxford University Press

STRING: finding tandem repeats in DNA sequences

Valerio Parisi 1,*, Valeria De Fonzo 2 and Filippo Aluffi-Pentini 3

1 Sez. INFM, 2 EuroBioPark, Univ. Roma ‘Tor Vergata’ Via della Ricerca Scientifica 1, 00133 Roma, Italy and 3 Dip. Metodi e Modelli Matematici, Univ. Roma ‘La Sapienza’ Via A. Scarpa 16, 00161 Roma, Italy

Received on November 4, 2002 ; revised on March 13, 2003 ; accepted on April 15, 2003

Motivation and results: The importance of Tandem Repeats in some genomes is now well established. We have reported elsewhere some interesting new results obtained by means of a preliminary program for finding Tandem Repeats in DNA sequences, together with a brief description of the basic ideas of the algorithm. We describe here a completely new program based only in part on those ideas, we briefly discuss the interpretation of the results, and, by way of example, we provide a few novel results relative to the parasites responsible of two re-emerging diseases, Plasmodium falciparum and Mycobacterium tuberculosis. Our program is portable, effective, powerful and fast: it can run on current desktop computers, and it finds all significant Tandem Repeats also in the longest segments of sequences in databases (up to millions of bases), in short times (minutes).

Availability: An academic version of the algorithm (full source listing in standard C language) can be freely downloaded (http://www.caspur.it/~castri/STRING/).

Supplementary information: Some illustrative figures and some sample results are provided as supplementary material at: http://www.caspur.it/~castri/STRING/

Contact: valerio.parisi{at}roma2.infn.it

* To whom correspondence should be addressed.


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
 Brief BioinformHome page
A. Merkel and N. Gemmell
Detecting short tandem repeats from genome data: opening the software black box
Brief Bioinform, September 1, 2008; 9(5): 355 - 366.
[Abstract] [Full Text] [PDF]

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
 BioinformaticsHome page
T. J. P. Sobreira, A. M. Durham, and A. Gruber
TRAP: automated classification, quantification and annotation of tandemly repeated sequences
Bioinformatics, February 1, 2006; 22(3): 361 - 362.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Boby, A.-M. Patch, and S. J. Aves
TRbase: a database relating tandem repeats to disease genes for the human genome
Bioinformatics, March 15, 2005; 21(6): 811 - 816.
[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.