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  The generalised k-Truncated Suffix Tree for time- and space-efficient searches in multiple DNA or protein sequences

Schulz, M. H., Bauer, S., & Robinson, P. N. (2008). The generalised k-Truncated Suffix Tree for time- and space-efficient searches in multiple DNA or protein sequences. International Journal of Bioinformatics Research and Applications: Ijbra, 4(1), 81-95. doi:10.1504/IJBRA.2008.017165.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-80B3-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-80B4-6
Genre: Journal Article

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 Creators:
Schulz, Marcel H.1, Author
Bauer, Sebastian, Author
Robinson, Peter N.2, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              

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Free keywords: suffi; x trees; biological sequence analysis; suffi; x array; bioinformatics; multiple DNA sequences; protein sequences.
 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.

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Language(s): eng - English
 Dates: 2008-01-01
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
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Title: International Journal of Bioinformatics Research and Applications : Ijbra
Source Genre: Journal
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Pages: - Volume / Issue: 4 (1) Sequence Number: - Start / End Page: 81 - 95 Identifier: ISSN: 1744-5485