A Genomic Sequence Matching Algorithm with Edge-base Quadtree Pattern Matching

• Main Authors: Chih-Yuan Chen, 陳志遠
• Other Authors: Show-Wei Leu
• Format: Others
• Language: zh-TW
• Published: 2005
• Online Access: http://ndltd.ncl.edu.tw/handle/65851832614229881825

碩士 === 國立臺灣海洋大學 === 電機工程學系 === 93 === Since the inception of Human Genome Project back in 1990s researchers in multiple disciplines have been seeking for highly efficient sequence alignment algorithms. Because a genome sequence can be regarded as a text string, many string matching algorithms can indeed be use for the genome sequencing tasks. However, many well-known, traditional string matching algorithms such as the Boyer More and the Knuth-Morris-Pratt (KMP), when used to match the genome sequences are often plagued by inefficiency, computational complexity, and consumption of huge memory space. Therefore, algorithms tailored for genomic sequencing have attracted a new generation of algorithm designers. In this thesis, we focus our attention on improving the existing algorithms for genome sequence matching. We have successfully reduced the huge memory consumption of the suffix tree method. Also, by introducing a new quadtree pattern matching we are able to avoid the highly complicated matching process of the ACGT-words tree algorithm. Last but not least, our method performs multi-pattern searching, which is beyond the capability of the algorithms we set out to improve.