跳到主要內容

臺灣博碩士論文加值系統

(18.205.192.201) 您好!臺灣時間:2021/08/05 11:00
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:林哲緯
研究生(外文):Che-Wei Lin
論文名稱:應用唯一標的法增進基因資料庫之定址速度與精準度
論文名稱(外文):Apply the Uni-Marker method to enhance performance and accuracy of genomic database mapping
指導教授:朱唯勤朱唯勤引用關係
指導教授(外文):Woei-Chyn Chu
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:醫學工程研究所
學門:工程學門
學類:生醫工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:52
中文關鍵詞:基因資料庫定址
外文關鍵詞:genomic databasemapping
相關次數:
  • 被引用被引用:0
  • 點閱點閱:127
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
人類基因體計畫(Human Genome Project, HGP)於公元2000年6月26日公佈了人類基因體的草圖。這個包含了染色體解析和DNA定序的重大工程,可以說是人類對自身了解的新里程碑。
隨著人類基因體草圖排序完成,「生物資訊」成為解讀基因體圖譜裡所隱藏奧秘之不可或缺的一門新興領域,生物資訊界學者近幾年來專注於研發新穎快速的演算法,用以處理分析大量的基因序列及蛋白質結構資料。預料以基因為主的研究將加速醫學科學對人類疾病的瞭解,產生高價值的醫學應用,同時加速生物資訊產業的建立。所以整合電腦與程式、資訊網路與基因體資料將成為生技產業發展的關鍵。
在人類30億鹼基序列中,定址出基因序列位於資料庫中之位置,是一門相當耗費時間與資源的工作。目前生物科學家主要是透過BLAST (Basic Local Alignment Search Tool)[2]方法完成。然而BLAST演算法的先天上設計著重於序列搜尋與排比,在基因資料庫定址的速度及精準度部分尚有改善空間。我們探討UM (Uni-Marker)[1]方法並改良其程式架構,應用於人類染色體基因序列資料庫定址上,期望在定址之速度與準確度方面達成更佳的效率。
UM方法可以運用四部個人電腦在二十個小時內成功定位一百六十萬條SNP (Single Nucleotide Polymorphism)序列在人類染色體上之位置。此方法經證實在序列定址速度與準確度方面遠超過NCBI (National Center for Biotechnology Information)[3]所提供之BLAST方法。
本論文擬應用UM演算法,針對人類染色體序列資料庫進行研究,並改寫其程式架構,方便使其適用於各種基因序列之快速定址。同時將系統建置於網路主機並整合GUI (Graphic User Interface),讓使用者可以透過網路執行我們的系統。
HGP (Human Genome Project) announced a rough draft of the human genome in Jun.26,2000. This human genome includes not only analysis of chromosome, but also the sequences of DNA. It is considered a great invention to human being.
“Bioinformatics” has become a rapidly developing domain to describing those unknown secret in Human genome. Researchers do their best in studying and developing fast algorithm to analyze huge genomic sequences and protein structures to increase our knowledge about ourselves. In order to do so, we need to integrate the key factors of computers, programs, network and genomic database in biotechnology developing.
Mapping address of genomic sequence on human genomic database consists of three billion nucleotides is a huge time and resource consuming job. Biologists use BLAST (Basic Local Alignment Search Tool) [2] to handle those jobs. However, BLAST performs well on sequence searching and alignment, it doesn’t deliver equally well performance nor accuracy on genomic database mapping as UM (Uni-Marker) [1] method does.
UM method could efficiently map 160 million SNP (Single Nucleotide Polymorphism) sequences on human genome in less than 20 hours CPU time. The method is much faster and more accurate than the NCBI (National Center for Biotechnology Information) [3] BLAST method.
This thesis adopts the concept of UM method and focuses on the research of human genome. In order to map other assignable sequences on human chromosome genome, we have modified and rebuilt the structure of UM program. By adding the GUI (Graphic User Interface) into the initial program and making it accessible via the internet. We expect the new application would enhance the performance and accuracy in genomic database mapping.
[1]Ming-Jing Hwang, Leslie Y.Y. Chen etc., Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences, 2002, Genome Res .
[2]Altschul S.F., Gish W. etc., Basic local alignment search tool, 1990, J.Mol.Biol.215.
[3]NCBI BLAST [http://www.ncbi.nih.gov/blast]
[4]Alexander Pertsemlidis, John W FondonIII etc., Having a BLAST with bioinformatics, Genome Biology 2001, 2(10):reviews2002.1–2002.10
[5]Antje Krause, Database search methods, Briefings in Bioinformatics 3(4): 342- 352 (2002).
[6]Liisa B. Koski and G. Brian Golding etc., The closest BLAST hit is often not the nearest neighbor,2001, Journal of Molecular Evol.2001 Jun;52(6):540-2.
[7]Aaron J. Sender, In this month;s genome technology: Academia Sinica’s BLAST buster turbocharges SNP mapping, 9/18/2002,
[http://www.genomeweb.com]
[8]Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919.
[9]David W. Mount, Bioinformatics: Sequence and Genome Analysis,
2000
[10]Gyntbia Gibas, Per Jambeck, Developing Bioinformatics Computer Skills, 2002
[11] Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8: 967-974
[12] Mott, R. 1998. Trace alignment and some of its applications. Bioinformatics 14: 92-97
[13] Schafer, A.J. and Hawkins, J.R. 1998. DNA variation and the future of human genetics. Nat. Biotech. 16: 33-39
[14]James D.Tisdall, Beginning Perl for Bioinformatics, 2002, O’RILLY
[15]Gyntbia Gibas, Per Jambeck, Developing Bioinformatics Computer Skill, 2001, O’RILLY
[16]R.Durbin, S.Eddy, A.Krogh, G.Mitchison, Biological sequence analysis,1998, Camvridge.
[17] Angela Telerski, An Anlysis of SNP Positions in Gene Regions of the Human Genome, June 1,2001
[18] Mammalian Gene Collection (MGC) [http://mgc.nci.nih.gov/]
[19] Franz Inc [www.franz.com/support/tutorials/knowbase.html]
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top