Searching gene and protein sequence databases.
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TL;DR
The classic algorithms for similarity searching and sequence alignment are described and good performance of these algorithms is critical to searching very large and growing databases.
Abstract
A large-scale effort to map and sequence the human genome is now under way. Crucial to the success of this research is a group of computer programs that analyze and compare data on molecular sequences. This article describes the classic algorithms for similarity searching and sequence alignment. Because good performance of these algorithms is critical to searching very large and growing databases, we analyze the running times of the algorithms and discuss recent improvements in this area.