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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.


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