Spectral Repeat Finder (SRF) is a program to find repeats using various digital signal processing (DSP) techniques on a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. The repeats can be contiguous, in which case they are termed tandem repeats, or not, in which case they are dispersed. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not.
In order to use the program, the user submits a sequence in various specified formats. The program's analysis is sent back to the user's web browser as single file containing information about the repeat unit, consensus pattern, region, copy number and score. It also contains links to view the Fourier spectrum and the detailed analysis of any particular repeat unit. The program can analyze sequence of any length.
Large sequences (>10 kb) take lot of time to be analyzed. Sequence information sent to the server is confidential and deleted after 5 days of program execution.
For the code of the program, contact Dr. Deepak Sharma