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STRING: finding tandem repeats in DNA sequences.
Valerio Parisi1, Valeria De Fonzo, Filippo Aluffi-Pentini
1Sez. INFM, EuroBioPark, Univ. Roma 'Tor Vergata' Via della Ricerca Scientifica 1, 00133 Roma, Italy. valerio.parisi@roma2.infn.it
Bioinformatics (Oxford, England)
|September 27, 2003
Summary
A new program efficiently identifies Tandem Repeats in DNA sequences, aiding research into diseases caused by Plasmodium falciparum and Mycobacterium tuberculosis. This tool offers fast and accurate analysis on standard computers.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Tandem Repeats play a significant role in various genomes.
- Previous work established preliminary findings on Tandem Repeat identification algorithms.
Purpose of the Study:
- To introduce a novel, efficient program for detecting Tandem Repeats in DNA sequences.
- To demonstrate the program's utility with examples from Plasmodium falciparum and Mycobacterium tuberculosis.
Main Methods:
- Development of a new algorithm for Tandem Repeat detection, partially based on prior ideas.
- Application of the program to analyze DNA sequences from key parasitic organisms.
Main Results:
- The program is portable, effective, powerful, and fast, running on desktop computers.
- It successfully identifies significant Tandem Repeats in large DNA sequences (millions of bases) within minutes.
- Novel results were obtained for Plasmodium falciparum and Mycobacterium tuberculosis.
Conclusions:
- The developed program provides a significant advancement in Tandem Repeat analysis.
- Its speed and efficiency make it suitable for analyzing extensive genomic datasets.
- The tool aids in understanding the genetic makeup of pathogens responsible for re-emerging diseases.