Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Int J Bioinform Res Appl. 2008;4(1):81-95.

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

Author information

  • 1Institute fur Medizinische Genetik, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.marcel.schulz@molgen.mpg.de

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.

PMID:
18283030
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Loading ...
    Write to the Help Desk