1. Lexa M, Valle G
Combining rapid word searches with segment-to-segment alignment for sensitive similarity detection, domain identification and structural modelling.
Meeting: BITS 2004 - Year: 2004
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Topic: Structural genomics
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 . Our interest in this area stems from the development of programs for fast searches with mismatches in large biological databases . 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.