Dissertation/ Thesis
Generalized pattern matching applied to genetic analysis. ; 通用性模式匹配在基因序列分析中的應用 ; CUHK electronic theses & dissertations collection ; Digital dissertation consortium ; Tong yong xing mo shi pi pei zai ji yin xu lie fen xi zhong de ying yong
| Τίτλος: | Generalized pattern matching applied to genetic analysis. ; 通用性模式匹配在基因序列分析中的應用 ; CUHK electronic theses & dissertations collection ; Digital dissertation consortium ; Tong yong xing mo shi pi pei zai ji yin xu lie fen xi zhong de ying yong |
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| Συνεισφορές: | Ni, Bing., Chinese University of Hong Kong Graduate School. Division of Computer Science and Engineering. |
| Έτος έκδοσης: | 2011 |
| Συλλογή: | The Chinese University of Hong Kong: CUHK Digital Repository / 香港中文大學數碼典藏 |
| Θεματικοί όροι: | Combinatorial analysis, Computational biology, Computer algorithms, DNA--Analysis--Data processing, Genetics--Methodology, Matching theory, Proteins--Analysis--Data processing, Computational Biology--methods, Sequence Analysis, DNA, Protein |
| Περιγραφή: | Approximate pattern matching problem is, given a reference sequence T, a pattern (query) Q, and a maximum allowed error e, to find all the substrings in the reference, such that the edit distance between the substrings and the pattern is smaller than or equal to the maximum allowed error. Though it is a well-studied problem in Computer Science, it gains a resurrection in Bioinformatics in recent years, largely due to the emergence of the next-generation high-throughput sequencing technologies. This thesis contributes in a novel generalized pattern matching framework, and applies it to solve pattern matching problems in general and alternative splicing detection (AS) in particular. AS is to map a large amount of next-generation sequencing short reads data to a reference human genome, which is the first and an important step in analyzing the sequenced data for further Biological analysis. The four parts of my research are as follows. ; In the first part of my research work, we propose a novel deterministic pattern matching algorithm which applies Agrep, a well-known bit-parallel matching algorithm, to a truncated suffix array. Due to the linear cost of Agrep, the cost of our approach is linear to the number of characters processed in the truncated suffix array. We analyze the matching cost theoretically, and .obtain empirical costs from experiments. We carry out experiments using both synthetic and real DNA sequence data (queries) and search them in Chromosome-X of a reference human genome. The experimental results show that our approach achieves a speed-up of several magnitudes over standard Agrep algorithm. ; In the fourth part, we focus on the seeding strategies for alternative splicing detection. We review the history of seeding-and-extending (SAE), and assess both theoretically and empirically the seeding strategies adopted in existing splicing detection tools, including Bowtie's heuristic and ABMapper's exact seedings, against the novel complementary quad-seeding strategy we proposed and the corresponding ... |
| Τύπος εγγράφου: | thesis |
| Περιγραφή αρχείου: | electronic resource; microform; microfiche; 1 online resource (xxi, 161 leaves : ill. (some col.)) |
| Γλώσσα: | English Chinese |
| ISBN: | 978-1-267-19937-9 1-267-19937-7 |
| Relation: | cuhk:344817; http://library.cuhk.edu.hk/record=b6075184 |
| Διαθεσιμότητα: | http://library.cuhk.edu.hk/record=b6075184 https://repository.lib.cuhk.edu.hk/en/item/cuhk-344817 |
| 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/) |
| Αριθμός Καταχώρησης: | edsbas.AF00F1D2 |
| Βάση Δεδομένων: | BASE |
| ISBN: | 9781267199379 1267199377 |
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