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Biological database indexing and its applications.

Cheung Ching Fung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 71-73). / Abstracts in English and Chinese. / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Biological Sequences --- p.2 / Chapter 1.2 --- User Queries on Biological Sequences --- p.4 / Chapter 1.3 --- Research Contributions --- p.6 / Chapter 1.4 --- Organization of Thesis --- p.6 / Chapter 2 --- Background --- p.7 / Chapter 2.1 --- What is a Suffix-Tree? --- p.7 / Chapter 2.2 --- Disk-Based Suffix-Trees --- p.9 / Chapter 3 --- Disk-Based Suffix Tree Constructions --- p.11 / Chapter 3.1 --- An Existing Algorithm: PrePar-Suff ix --- p.11 / Chapter 3.1.1 --- "Three Issues: Edge Splitting, Random Access and Data Skew" --- p.13 / Chapter 3.2 --- DynaCluster-Suffix: A New Novel Disk-Based Suffix-Tree Construction Algorithm --- p.18 / Chapter 4 --- Suffix Links Rebuilt --- p.29 / Chapter 4.1 --- Suffix-links and Least Common Ancestors --- p.29 / Chapter 5 --- q-Length Exact Sequence Matching --- p.35 / Chapter 5.1 --- q-Length Exact Sequence Matching by Suffix-Tree --- p.35 / Chapter 6 --- Implementation --- p.38 / Chapter 6.1 --- System Overview --- p.38 / Chapter 6.1.1 --- Index Builder --- p.39 / Chapter 6.1.2 --- Exact Query Processor --- p.39 / Chapter 6.1.3 --- Suffix Links Regenerator --- p.40 / Chapter 6.1.4 --- Tandem Repeats Finder --- p.40 / Chapter 6.2 --- Data Structures --- p.40 / Chapter 6.2.1 --- Representation of a Node --- p.40 / Chapter 6.2.2 --- An Alternative Node Representation --- p.42 / Chapter 6.2.3 --- Representation of a Leaf --- p.43 / Chapter 6.3 --- Buffering --- p.44 / Chapter 6.3.1 --- Page Format --- p.44 / Chapter 6.3.2 --- Address Translation --- p.45 / Chapter 6.3.3 --- Page Replacement Strategies --- p.45 / Chapter 7 --- A Performance Studies --- p.48 / Chapter 7.1 --- When Everything Can be Held In Memory --- p.52 / Chapter 7.2 --- When Main Memory Is Limited --- p.54 / Chapter 7.3 --- The Effectiveness of DNA Lengths with Fixed Memory Sizes . --- p.56 / Chapter 7.4 --- The Effectiveness of Memory Sizes --- p.57 / Chapter 7.5 --- Answering q-Length Exact Sequence Matching Queries --- p.60 / Chapter 7.6 --- Suffix Link Rebuilt --- p.61 / Chapter 8 --- Conclusions and Future Works --- p.69 / Chapter 8.1 --- Conclusions --- p.69 / Chapter 8.2 --- Future Works --- p.70 / Bibliography --- p.71

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_323872
Date January 2002
ContributorsCheung, Ching Fung., Chinese University of Hong Kong Graduate School. Division of Systems Engineering and Engineering Management.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, viii, 73 leaves : ill. ; 30 cm.
RightsUse of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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