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Enhanced Suffix Trees for Very Large DNA Sequences

Title:

Enhanced Suffix Trees for Very Large DNA Sequences

Fan, Si Ai (2011) Enhanced Suffix Trees for Very Large DNA Sequences. Masters thesis, Concordia University.

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Abstract

Recent advances in bio-technology have provided rapid accumulation of biological DNA sequence data. New techniques are required for fast, scalable, and versatile processing of such data.
Suffix tree (ST) is a data structure used for indexing genome data. This, however, comes with a price: it occupies a space that is about 10 times more than the input size. Existing disk-based ST index techniques either suffer from data skew problem, like TDD and HST, or are not space efficient for very large sequences, like TRELLIS and B2ST. We propose a new disk-based ST index, called Compact Binary Suffix Tree (CBST), together with a construction algorithm, which can support DNA sequences of size up to 256 terabyte. The results of our numerous experiments indicated that, compared to existing ST and suffix array techniques, CBST is superior in speed, space requirement, and scalability. It is the fastest among the disk-based techniques for very large sequences.

Divisions:Concordia University > Faculty of Engineering and Computer Science > Computer Science and Software Engineering
Item Type:Thesis (Masters)
Authors:Fan, Si Ai
Institution:Concordia University
Degree Name:M. Comp. Sc.
Program:Computer Science
Date:August 2011
Thesis Supervisor(s):Shiri, Nematollaah
Keywords:Suffix Tree, DNA, Sequence, Suffix Array, External, Binary Suffix Tree
ID Code:35799
Deposited By:SI AI FAN
Deposited On:21 Nov 2011 11:50
Last Modified:09 Nov 2012 18:06
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