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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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 Urheber:
Schulz, Marcel H.1, Autor
Bauer, Sebastian, Autor
Robinson, Peter N.2, Autor           
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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Schlagwörter: suffi; x trees; biological sequence analysis; suffi; x array; bioinformatics; multiple DNA sequences; protein sequences.
 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2008-01-01
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
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Titel: International Journal of Bioinformatics Research and Applications : Ijbra
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 4 (1) Artikelnummer: - Start- / Endseite: 81 - 95 Identifikator: ISSN: 1744-5485