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1 中草藥生物資訊與程式設計謝長奇 #37125

2 授課資料教學目標教導學生于生物資訊學, 並指導學生搜尋生物資訊利用生物資訊相關軟體與建構之生物資訊程式與計算平台授課方式電腦教室上機實習及課堂教學教學大樓 5F 視聽電腦教室

3 授課資料評分標準出席狀況 :10 % 上課態度 :20 % 學習成果 ( 隨堂考期中考期末考 ):70 % 參考書目 Introduction to Bioinformatics. Stephen A. Krawetz and David D. Womble Humana Press 基礎生物資訊實務李炎編著 2002 藝軒出版社生物資訊入門陳進和等編譯 2003 藝軒出版社 Beginning Perl for Bioinformatics. James D. Tisdall O'Reilly Press Mastering Perl for Bioinformatics. James D. Tisdall O'Reilly Press 生物資訊學電腦技術林仲彥李士傑陳淑華 OSB-TW 2002 歐萊禮

4 基礎生物資訊實務 ( 附光碟 )( 第二版 ) 本書主要以分子生物學的觀念, 介紹如何利用網路上免費的生物資訊工具如何將片段 DNA 查出它的可能蛋白質為何? 此蛋白質的可能 3D 結構為何? 或是它是否含有表現段 -exon 或插入段 intron? 有否含 trna mrna 或 rrna 片段? 幾個片段的胺基酸排序之間有否演化上的關連性? 並繪出演化樹

5 課程內容次數教學內容 Introduction NCBI and Other biomedical website Nucleic Acid Sequence Analysis and Information BLAST and Sequence alignment Phylogenic Analysis The Evolution from Sequence Information Genome Information Resources Statistical Analysis Med-Exam

6 課程內容次數教學內容 Perl programming introduction Perl programming in bioscience Perl programming in sequence search Perl programming in sequence analysis Perl programming in restriction map and virtual gel Perl programming in Genbank Perl programming in BLAST Perl programming in ClastalW Final exam

7 課程關連圖生物化學分析化學藥理學多元市場經營推廣新資源新產品開發中草藥資源中草藥生物資訊藥材資源鑑定分子生物學生物技術體學 ( 組學 ) 中草藥系統演化藥理毒理模型預測

8 課程學習路徑圖 DNA Database RNA protein In house design Analysis tools Sequence Phylogenic Evolution Public domain Bioinformation Knowledge

9 Bioinformatics introduction

10 生物資訊學利用應用數學資訊學統計學和電腦科學的方法研究生物學的問題目前的生物資訊學生物資訊學基本上只是分子生物學與資訊技術 ( 尤其是網際網路技術 ) 的結合體生物資訊學的研究材料和結果就是各種各樣的生物學數據, 其研究工具是電腦, 研究方法包括對生物學數據的搜索 ( 收集和篩選 ) 處理 ( 編輯整理管理和顯示 ) 及利用 ( 計算模擬 ) 目前主要的研究方向有 : 序列比對, 基因識別, 基因重組, 蛋白質結構預測, 基因表達, 蛋白質反應的預測, 以及建立進化論的模型

11 生物資訊學生物學技術往往生成大量的嘈雜數據與數據挖掘類似, 生物資訊學利用數學工具從大量數據中提取有用的生物學資訊生物資訊學所要處理的典型問題包括 : 重新組裝在散彈法 DNA 測序過程中被打散的 DNA 序列, 從蛋白質的胺基酸序列預測蛋白質結構, 利用 mrna 微陣列或質譜儀的數據檢驗基因調控的假說

12 What is bioinformatics? formatics.html

13 What is bioinformatics The term was first coined in 1988 by Dr. Hwa A. Lim (HAL), and is commonly known as the Father of Bioinformatics. The original definition was : a collective term for data compilation, organisation, analysis and dissemination

14 What is bioinformatics The use of computers in solving information problems in the life sciences, mainly, it involves the creation of extensive electronic databases on genomes, protein sequences, etc. It involves techniques such as the threedimensional modeling of biomolecules and biologic systems.

15 Why study bioinformatics variety sources of data make the data easily and universally interpretable by scientists post-genomic era

16 Progressing history Mendel proved his laws of hereditary with varieties of peas and flowers in 1865 The first protein to be sequenced insulin The first complete sequencing of an enzyme, ribonuclease in 1960 To the sequencing of the first complete genome (Haemophilus influenzae) ) published in 1995 moved on to technologies permitting the sequencing, recombination and cloning of DNA

17 The Human Genome Project In 1990 the unveiling of the Human Genome Project (HGP) by the United States Department of Energy (DoE) and the National Institutes of Health Goals: to identify all chemical base pairs and all genes that make up the 23 chromosome pairs found in human DNA To develop the next generation of methods for simulating cellular behaviour and pathways

18 The Human Genome Project Collaboration of 20 groups across the world The results would be free and data release would be rapid To identify every base pair in the genome - there are 3 x 10 9 To assign genes and what they code for or not Potentially revolutionise biomedical research

19 The Human Genome Project The initial estimates were that the human genome comprised some 100,000+ genes - now we know there are only 30-40,000 only twice as many as found in a worm or a fly

20 Gene Open Reading Frames The complex splicing techniques of higher organisms means each protein-coding gene generates between 3 and 6 proteins = 50,000 to 500,000 proteins per individual

21 Gene The idea that 1 gene = 1 protein is clearly wrong The gene structure and the components that regulate its expression must be much more complex than previously thought Still have roughly 100,000 genes of microbes, plants and animals whose functions are still to be revealed

22 Systemic biology Human ~40,000 genes ~100, ,000 splice variants ~500,000-2,000,000 proteins (polypeptides) ~ metabolic pathways

23 Systemic biology Molecular interaction complexity

24 Molecular Interaction Maps

25 Systemic biology Evolutionary complexity elimination series

26 The omics revolution Genomics the sequencing and annotation of genomes Functional and structural genomics the comparison and characterisation of genomes of different species Proteomics the description of the complete set of proteins a particular genome codes

27 Model organisms Cheap Plentiful Short generation times Easily manipulated Test novel drug candidates Illustrating which genes, and therefore which proteins, are responsible for which phenotype/disease 85% genetic similarity between the mouse and human genome

28 Computer science come into The HGP has brought to light the limitations of traditional lab work Bioinformaticists act to bridge the gap between the data stored and its biological significance

29 Bioinformatics Tools GenBank - genes, proteins, genomes Similarity Search tools: BLAST, VAST Alignment: CLUSTAL Protein families: Pfam, ProDom Protein Structures: PDB, RasMol Whole Genomes: UCSC, Entrez Genomes Human Mutations: OMIM Biochemical Pathways: KEGG Integrated tools: Biology Workbench, BCM Search Launcher

30 Entrez Databases contain more than just DNA & protein sequences

31 Bioinformatics Data DNA Sequences Genes Location, introns, exons, function, etc. Gene products RNA, Proteins Pathways Signaling, metabolic, genomic, etc.

32 Bioinformatics Data Experimental Gene expression, knockouts, etc. Literature Diseases, viruses, bacteria Organisms Textbooks Expert knowledge Unpublished Insights

33 親緣關係

34 生物資訊工具美國國家生技資訊中心 NCBI(National Center For Biotechnology Information): 專門搜集排序完全完成的基因資料庫 : 病毒基因組資料庫 :

35 生物資訊工具 RNA 類病毒 (viroid 即無外殼的 RNA) 資料庫 : 質體資料庫 : 酵母菌資料庫 :

36 生物資訊工具胞器資料庫 : 人類粒線體資料庫 ( 共 37 個基因 ): 以不同生物分別的基因資料庫 :

37 演化分類工具 index.html

38 Perl

39 Perl programming for bioinformatics Perl language veperl/ Perl/Windows/5.8/ActivePerl MSWin32-x msi (Win, x86)

40 Perl program Perl 學習手札 Perl 學習手札全文

41 What is Perl? Perl is an acronym that stands for Practical Extraction and Reporting Language) Larry Wall began work on Perl in 1987 Perl was originally named "Pearl", after the Parable of the Pearl from the Gospel of Matthew Larry Wall claims that he considered (and rejected) every three- and four-letter word in the dictionary Engraving by John Everett Millais illustrating the parable of the Pearl of Great Price. Published in Parables of Our Lord, 1864

42 The end

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untitled Course No. 00333280 will lead you Computational Biology / Bioinformatics? NIH Computational Biology (The development and application of data-analytical and theoretical methods, mathematical modeling and