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
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_323872 |
| Date | January 2002 |
| Contributors | Cheung, Ching Fung., Chinese University of Hong Kong Graduate School. Division of Systems Engineering and Engineering Management. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | print, viii, 73 leaves : ill. ; 30 cm. |
| Rights | Use 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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