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CS5238 Combinatorial methods in bioinformatics 2004/2005 Semester 1
Lecture 8: Finding structural similarities among proteins (II)
Lecturer: Prof Jean-Claude Latombe
Scribe: Cheng Chi Kan, Lee Pern Chern and Moritz Buck
1 Voting scheme with hash table
Many-to-many comparisons are evaluated when we align protein structures. In order to avoid repetition, a better
organization of computation is necessary. This could be achieved by pre-computing the indexes of proteins and
arranging them in a hash table. Then, queries are evaluated based on a voting scheme using the hash table. This
voting scheme replaces the seed generation process.
In this lecture, we look into the voting scheme used in 3dSEARCH . The algorithm is based on the concept of
geometric hashing  developed in the eld of computer vision. The basic idea is to represent all secondary structure
elements (SSEs) from all target proteins with a large, highly redundant hash (or index) table. Once the table ...
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