Abstract: The identification of repeats is an essential step for genome analysis and annotation, but is not easy because repeats tend to be little conserved during evolution. This particular aspect of repeats makes very difficult the identification of homologous sequences that diverged significantly, both within the same genome and between genomes of different organisms.

Abstract: The most popular alignment and similarity search techniques are based on the classical Smith-Waterman scoring scheme. Conservation of a single structural or functional feature between proteins may be undetectable, because the similarities tend to persist only in the key areas, consisting of residues dispersed in a non-trivial manner. We propose a novel method that finds occurrences of short similar words common to the studied sequences and handles the identified matches in a manner similar to segment-to-segment alignment [2]. Our interest in this area stems from the development of programs for fast searches with mismatches in large biological databases [1]. As shown here, these programs can support large database searches that lead to automatic domain detection, sequence annotation. The use of this technique in fold-recognition and structure prediction is being studied.

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