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Bioinformatics Advance Access published online on February 19, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth103
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 4, 2003
Revised August 31, 2003
Accepted November 30, 2003

Article

Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation

Deepak Sharma 1, Biju Issac 2, G. P. S. Raghava 2, R. Ramaswamy 3*

1 Department of Biotechnology, All India Institute of Medical Sciences, New Delhi-110029, India
2 Institute of Microbial Technology, Chandigarh-160036, India
3 School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India; School of Information Technology, Jawaharlal Nehru University, New Delhi-110067, India

* To whom correspondence should be addressed. E-mail: r.ramaswamy{at}mail.jnu.ac.in.


  Abstract

Motivation: Repetitive DNA sequences, besides having a variety of regulatory functions, are one of the principal causes of genomic instability. Understanding their origin and evolution is of fundamental importance for genome studies. The identification of repeats and their units helps in deducing the intra-genomic dynamics as an important feature of comparative genomics. A major difficulty in identification of repeats arises from the fact that the repeat units can be either exact or imperfect, in tandem or dispersed, and of unspecified length.

Results: The Spectral Repeat Finder (SRF) program circumvents these problems by using a discrete Fourier Transformation (FT) to identify significant periodicities present in a sequence. The specific regions of the sequence that contribute to a given periodicity are located through a sliding window analysis, and an exact search method is then used to find the repetitive units. Efficient and complete detection of repeats is provided together with interactive and detailed visualization of the spectral analysis of input sequence. We demonstrate the utility of our method with various examples that contain previously unannotated repeats. A web server has been developed for convenient access to the automated program.

Availability: The web server is available at http://www.imtech.res.in/raghava/srf and http://www2.imtech.res.in/raghava/srf.


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