Summary: Reference­Based Alignment in Large Sequence Databases
Panagiotis Papapetrou 1 , Vassilis Athitsos 2 , George Kollios 1 , and Dimitrios Gunopulos 3,4
1 Computer Science Department, Boston University
2 Computer Science and Engineering Department, University of Texas at Arlington
3 Department of Informatics and Telecommunications, University of Athens
4 Computer Science and Engineering Department, UC Riverside
ABSTRACT
This paper introduces a novel method, called Reference­Based String
Alignment (RBSA), that speeds up retrieval of optimal subsequence
matches in large databases of sequences under the edit distance and
the Smith­Waterman similarity measure. RBSA operates using the
assumption that the optimal match deviates by a relatively small
amount from the query, an amount that does not exceed a prespec­
ified fraction of the query length. RBSA has an exact version that
guarantees no false dismissals and can handle large queries effi­
ciently. An approximate version of RBSA is also described, that
achieves significant additional improvements over the exact ver­
sion, with negligible losses in retrieval accuracy. RBSA performs
filtering of candidate matches using precomputed alignment scores
between the database sequence and a set of fixed­length reference

Source: Athitsos, Vassilis - Department of Computer Science and Engineering, University of Texas at Arlington

Collections: Computer Technologies and Information Sciences