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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



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ID: 404862.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
The generalised k-Truncated Suffix Tree for time- and space-efficient searches in multiple DNA or protein sequences
Authors:Schulz, Marcel H.; Bauer, Sebastian; Robinson, Peter N.
Language:English
Date of Publication (YYYY-MM-DD):2008-01-01
Title of Journal:International Journal of Bioinformatics Research and Applications : Ijbra
Volume:4
Issue / Number:1
Start Page:81
End Page:95
Copyright:© 2008 Inderscience Enterprises Limited. All rights reserved.
Review Status:not specified
Audience:Experts Only
Abstract / Description: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.
Free Keywords:suffi; x trees; biological sequence analysis; suffi; x array; bioinformatics; multiple DNA sequences; protein sequences.
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
External Affiliations:1.Institut für Medizinische Genetik, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
Identifiers:URL:http://www.inderscience.com/search/index.php?actio...
DOI:10.1504/IJBRA.2008.017165
ISSN:1744-5485
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