跳到主要內容

簡易檢索 / 詳目顯示

回結果列表
研究生： 陳中興
Zhong-Xing Cheng
論文名稱： 用Pfam-A建議BLAST之計分表(Scoring Matrix)與空格罰分(Gap Penality)
指導教授： 張憶壽
I-Shou Chang
口試委員:
學位類別： 碩士
Master
系所名稱： 理學院 - 數學系
Department of Mathematics
畢業學年度： 89
語文別： 中文
論文頁數： 47
中文關鍵詞： 生物資訊 、序列比對 、計分表 、格罰分
外文關鍵詞： bioinformatics, equence alignment
相關次數： 點閱：18  下載：0 
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報


    • 本文之目的乃是以Karlin & Altschul之理論為基礎,提出以物種為考慮因素的新計分表與空格罰分。並以BLOSUM系列為比較對象,發現在Pfam資料庫中,大腸桿菌(Escherichia coli)、線蟲(Caenorhabditis elegans)
    、果蠅(Drosophila)、老鼠(Mus musculus)與人類(Homo sapiens)等五物種所形成的新計分表都介於BLOSUM 35 至 BLOSUM 40之間。

    2 計分模型與HMM 7 2.1 BLOSUM .................................................7 2.2 Alignment Algorithm ....................................9 2.3 HMM and Pfam ..........................................11 3 理論與其應用 13 4 例子:人與果蠅 16 5 結果與討論 19 5.1 Result ................................................19 5.2 Discussion ............................................20 A 附錄:資料 21 B 附錄:表格 23 C 附錄:圖表 34

    1.Altschul,S.F.,Gish,W.,Miller,W.,Myers,E.W. and Lipman,D.J.(1990)Basic local alignment search tool.Journal of Molecular Biology 215：403-410
    2.Altschul,S.F.,Madden,T.L.,Schaffer,A.A.,Zhang,J.,Zhang,Z.,Miller,W. and Lipman,D.J.(1997)Gapped BLAST and PSI-BLAST：a new generation of protein database search programs.Nucleic Acids Research 25：3389-3402
    3.Pearson,W.R. and Lipman,D.J.(1988)Improved tools for biological sequence comparison.Proceedings of the National Academy of Sciences of the USA 4:2444-2448
    4.Rabiner,L.R. and Juang,B.H.(1993)Foundamentals of Speech Recognition.Prentice-Hall.
    5.Krogh,A.(1994)Hidden Markov models for labeled sequences.In Proceedings of the 12th IAPR International Conference on Pattern Recognition,140-144.IEEE Computer Society Press.
    6.Liu,J.S.,Neuwald,A.F. and Lawrence,C.E.(1995)Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies.Journal of the American Statistical Association 90:1156-1170
    7.Henikoff,S. and Henikoff,J.G.(1991)Automated assembly of protein blocks for database searching.Nucleic Acids Research 19：6565-6572
    8.Henikoff,S. and Henikoff,J.G.(1992)Amino acid substitution matrices from protein blocks.Proceedings of the National Academy of Sciences of the USA 89:10915-10919
    9.Dayhoff,M.O.,Schwartz,R.M. and Orcutt,B.C.(1978)A model of evolutionary change in proteins.In Dayhoff,M.O.,ed.,Atlas of Protein Sequence and Structure,volume 5,supplement 3.National Biomedical Research Foundation,Washington D.C. pp.345-352
    10.Sonnhammer,E.L.,Eddy,S.R. and Durbin,R.(1997)Pfam:A comprehensive database of protein families based on seed alignments.Proteins 28:405-420
    11.Gotoh,O.(1982)An improved algorithm for matching biological sequences.Journal of Molecular Biology 162：705-708
    12.Durbin,R.,Eddy,S.R.,Krogh,A. and Mitchison,G.(1998)Biological sequence analysis.Cambridge University Press：Cambridge,UK.
    13.Needleman,S.B. and Wunsch,C.D.(1970)A general method applicable to the search for similarities in the amino acid sequence of two proteins.Journal of Molecular Biology 48：443-453
    14.Smith,T.F. and Waterman,M.S.(1981)Identification of common molecular subsequences.Journal of Molecular Biology 147：195-197
    15.Thompson,J.D.,Higgins,D.G. and Gibson,T.J.(1994)CLUSTAL W：improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position specific gap penalties and weight matrix choice.Nucleic Acids Research 22：4673-4680
    16.Karlin,S. and Altschul,S.F.(1990)Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.Proceedings of the National Academy of Sciences of the USA 87：2264-2268
    17.Karlin,S.,Dembo,A. and Kawabata,T.(1990)Statistical composition of high-scoring segments from molecular sequences.The Annals of Statistics 18：571-581

    QR CODE
    :::