具序列比對與資料壓縮功能之基因體資料庫系統設計

Abstract

隨著人類基因體計畫的初步完成，後基因體時代正逐漸來臨，人類的序列圖譜雖然已被解開，卻不代表已完全了解每個序列片段所扮演的角色，它們的功能仍然需要被進一步地分析與研究。另一方面，因序列資料的快速擴增，資料整理與儲存議題更顯得日趨重要。本篇論文在探討並實作出一套基因體資料庫系統，供使用者儲放與管理序列資料。此系統最大的特色在於它整合了序列比對與資料壓縮的功能。藉由嵌入NCBI提供的程式- blastall，它能將使用者上傳的序列作比對，尋找出該序列在基因體相對應的位置；此外，該系統針對序列之間的差異部份作編碼，有效地將資料壓縮，減少儲存的空間。同時，它提供多樣化的查詢功能。使用者可依檢體編號、GI、序列位置等查詢方式，快速地搜尋到他們所感興趣的序列資料。

With the initial completion of Human Genome Project, the post-genomic era is coming. Although the genome map of human has been decoded, the roles that each segment of sequences acts are not totally discovered. Their actually functions are still needed to be analyzed and researched. On the other hand, with the rapid expansion of sequence information, the issues of data compilation and data storage are increasingly important. In this thesis, a “Human Genome Database System” is designed and implemented in National Taiwan University Hospital (NTUH). By accessing this system, users can store and manage the experimental sequence data. The greatest achievement of this system is that it integrates the modules of sequence alignment and data compression. By embedding with the NCBI alignment program- blastall, it automatically aligns the uploaded sequences and searches for the corresponding genomic positions. Besides, the system encodes the differences between sequences, effectively compresses them and decreases the demand of storage space. At the same time, it offers a variety of query methods. Users can quickly access the interesting data by inputting the keywords of specimen number, GI and sequence position, etc.