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We use a fast algorithm to search for repeating fragments
within protein sequences. The technique is based on an extension
of the Smith-Waterman algorithm that allows the calculation of
sub-optimal alignments of a sequence against itself. We are able to
estimate the statistical significance of all sub-optimal 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