REPRO (Protein Repeats Analysis) is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.
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George RA. and Heringa J. (2000)
The REPRO server: finding protein internal sequence repeats through the web
Trends Biochem. Sci. 25, 515-517.