We use a fast algorithm to search for repeating fragments
within protein sequences. The technique is based on an extension
of the SmithWaterman algorithm that allows the calculation of
suboptimal alignments of a sequence against itself. We are able to
estimate the statistical significance of all suboptimal alignment
scores. We also rapidly determine the length of the repeating fragment
and the number of times it is found in a sequence.
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Matteo Pellegrini

