Internal Repeats Finder
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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.
Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D. (1999)
J Mol Biol
293, 151 "A census of protein repeats"
Pellegrini M, Marcotte EM, Yeates TO. "A fast algorithm for genome-wide analysis of proteins with repeated sequences."
. 1999 Jun 1;35(4):440-6.