The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences
by Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 4, No. 1, 2008

Abstract: Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional to n independent of the length of the sequences, and are thus attractive for a variety of applications. Here, we present an algorithm termed the generalised k-Truncated Suffix Tree (kTST), that represents an adaption of Ukkonen's linear-time suffix tree construction algorithm. The kTST algorithm creates a k-deep tree in linear time that allows rapid searches for short patterns of length of up to k characters. The kTST can offer advantages in computational time and memory usage for searches for short sequences in DNA or protein sequences compared to other suffix-based algorithms.

Online publication date: Sun, 17-Feb-2008

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