The program REPRO (Heringa and Argos, 1993) 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. The REPRO program operates in two steps:
- Calculation of a list of N top-scoring non-overlapping local alignments. This is the SLOW step. The parameter N should be specified by the user.
- Graph-based clustering of M top-alignments to assemble the repeat sets. If you have completed step 1, then continue to Step 2
Documentation: an introduction to repro as well as a user guide, sample results, who to ask for help and references can be found here.
George RA. and Heringa J. (2000) The REPRO server: finding protein internal sequence repeats through the web. Trends Biochem. Sci. 25, 515-517.