中草藥生物資訊 與程式設計 - d'trendsintroduction to bioinformatics. stephen a....
TRANSCRIPT
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
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 2003. 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. 2001.
O'Reilly Press � Mastering Perl for Bioinformatics. James D. Tisdall. 2003.
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
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。
課程內容
Med-Exam9
Statistical Analysis8
Genome Information Resources7
The Evolution from Sequence Information6
Phylogenic Analysis5
BLAST and Sequence alignment4
Nucleic Acid Sequence Analysis and Information3
NCBI and Other biomedical website2
Introduction1
教 學 內 容次數
課程內容
Final exam18
Perl programming in ClastalW17
Perl programming in BLAST16
Perl programming in Genbank15
Perl programming in restriction map and virtual gel14
Perl programming in sequence analysis13
Perl programming in sequence search12
Perl programming in bioscience11
Perl programming introduction10
教 學 內 容次數
課程關連圖
中草藥資源
中草藥生物資訊
生物化學
分析化學
藥理學
分子生物學
生物技術
體學(組學)
藥理、毒理模型預測
中草藥系統演化
藥材資源鑑定
新資源、新產品開發
多元市場經營推廣
課程學習路徑圖
Database
DNA proteinRNA
Analysis tools
Sequence EvolutionPhylogenic
Bioinformation
Knowledge
Public domainIn house design
Bioinformatics
introduction
生物資訊學生物資訊學生物資訊學生物資訊學
� 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。
生物資訊學生物資訊學生物資訊學生物資訊學
�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。
What is bioinformatics?
� http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html
� http://www.bioinformatics.vg/what-is-bioinformatics.shtml
� http://www.biology.gatech.edu/graduate-programs/bioinformatics/new/whatis.php
� http://bioinformatics.org/faq/� http://www.bioinfo-online.net/modules/faq/
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”
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 three-dimensional modeling of biomoleculesand biologic systems.
Why study bioinformatics
� variety sources of data� make the data easily and universally
interpretable by scientists� post-genomic era
Progressing history
� Mendel proved his laws of hereditary with varieties of peas and flowers in 1865
� The The The The first protein to be sequenced first protein to be sequenced first protein to be sequenced first protein to be sequenced – insulininsulininsulininsulin� The The The The first complete sequencing of an enzyme, first complete sequencing of an enzyme, first complete sequencing of an enzyme, first complete sequencing of an enzyme,
ribonucleaseribonucleaseribonucleaseribonuclease in 1960in 1960in 1960in 1960� To the sequencing of the first complete genome To the sequencing of the first complete genome To the sequencing of the first complete genome To the sequencing of the first complete genome
((((HaemophilusHaemophilusHaemophilusHaemophilus influenzaeinfluenzaeinfluenzaeinfluenzae) published in 1995) published in 1995) published in 1995) published in 1995� moved on to technologies permitting the
sequencing, recombination and cloning of DNA
The Human Genome Project
� In 1990 the unveiling of the Human Genome In 1990 the unveiling of the Human Genome In 1990 the unveiling of the Human Genome In 1990 the unveiling of the Human Genome Project (HGP) by the United StatesProject (HGP) by the United StatesProject (HGP) by the United StatesProject (HGP) by the United StatesDepartment of Energy (DoE) and the National Institutes of Health
� Goals:Goals:Goals: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 To develop the next generation of methods To develop the next generation of methods To develop the next generation of methods for simulating cellular behaviour and pathwaysfor simulating cellular behaviour and pathwaysfor simulating cellular behaviour and pathwaysfor simulating cellular behaviour and pathways”
The Human Genome Project
� Collaboration of 20 groups across the world� The results would be free and data release The results would be free and data release The results would be free and data release The results would be free and data release
would be rapidwould be rapidwould be rapidwould be rapid� To identify every base pair in the genome -
there are 3 x 109
� To assign genes and what they code for or not
� Potentially revolutionise biomedical research
The Human Genome Project
� The initial estimates were that the human The initial estimates were that the human The initial estimates were that the human The initial estimates were that the human genome comprised some 100,000+ genes genome comprised some 100,000+ genes genome comprised some 100,000+ genes genome comprised some 100,000+ genes ----now we know there are only 30now we know there are only 30now we know there are only 30now we know there are only 30----40,00040,00040,00040,000
� only twice as many as found in a worm or a only twice as many as found in a worm or a only twice as many as found in a worm or a only twice as many as found in a worm or a flyflyflyfly
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
Gene
� The idea that 1 gene = 1 protein is clearly wrongwrongwrongwrong
� 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
Systemic biology
� Human� ~40,000 genes� ~100,000-150,000 splice variants� ~500,000-2,000,000 proteins (polypeptides)� ~600-1000 metabolic pathways
Systemic biology
� Molecular interaction complexity
Molecular Interaction Maps
http://discover.nci.nih.gov/mim/index.jsp
Systemic biology
� Evolutionary complexity� elimination series
http://www.ucmp.berkeley.edu/exhibit/phylogeny.html
The ‘omics’ revolution
� GenomicsGenomicsGenomicsGenomics – the sequencing and annotation of genomes
� Functional and structural genomicsFunctional and structural genomicsFunctional and structural genomicsFunctional and structural genomics – the comparison and characterisation of genomes of different species
� ProteomicsProteomicsProteomicsProteomics – the description of the complete set of proteins a particular genome codes
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
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
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
Entrez Databases contain more than just DNA & protein sequences
Bioinformatics Data
� DNA Sequences� Genes
� Location, introns, exons, function, etc.� Gene products
� RNA, Proteins� Pathways
� Signaling, metabolic, genomic, etc.
Bioinformatics Data
� Experimental� Gene expression, knockouts, etc.
� Literature� Diseases, viruses, bacteria� Organisms� Textbooks
� Expert knowledge� Unpublished� Insights
親緣關係http://www.pbs.org/wgbh/nova/israel/family.html
生物資訊工具
�美國國家生技資訊中心NCBI（National Center For Biotechnology Information）：http://www.ncbi.nlm.nih.gov/
�專門搜集排序完全完成的基因資料庫：http://www-nbrf.georgetown.edu/
�病毒基因組資料庫：� http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html� http://www.cbs.dtu.dk/services/EasyGene/� http://www.ebi.ac.uk/genomes/
生物資訊工具
� RNA類病毒 (viroid—即無外殼的RNA) 資料庫：� http://subviral.med.uottawa.ca/cgi-bin/home.cgi?oldURL=1� http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/
� 質體資料庫：� http://www.genomics.ceh.ac.uk/plasmiddb/� http://plasmid.hms.harvard.edu/� http://beckmancenter.ahc.umn.edu/cgi-bin/plasmidlookup.pl� http://gind-db.ucsf.edu:8000/cgi-bin/Plasmid/main_menu2.cgi� http://bccm.belspo.be/newsletter/8-00/bccm02.htm
� 酵母菌資料庫：� http://db.yeastgenome.org/cgi-bin/seqTools� http://mips.gsf.de/genre/proj/yeast/� http://www.ncyc.co.uk/search.php� http://genome-www.stanford.edu/
生物資訊工具
� 胞器資料庫：� http://organelledb.lsi.umich.edu/� http://www.ebioinfogen.com/biobase/organelle/
� 人類粒線體資料庫 (共37個基因)：� http://www.mitomap.org/� http://evogen.jgi.doe.gov/cgi-
bin/Mt_gene_order_browser.cgi� http://www.genpat.uu.se/mtDB/� http://www.hmdb.uniba.it/hmdb/index.jsp� http://www.smgf.org/pages/mtdatabase.jspx
� 以不同生物分別的基因資料庫：� http://restools.sdsc.edu/biotools/biotools10.html
演化、分類工具
� http://www.ucmp.berkeley.edu/index.html
� http://www.species2000.org/� http://evolution.berkeley.edu/
Perl
Perl programming for bioinformatics
� Perl language� http://www.perl.org� http://www.bioperl.org� http://www.activestate.com/products/acti
veperl/� http://downloads.activestate.com/Active
Perl/Windows/5.8/ActivePerl-5.8.8.820-MSWin32-x86-274739.msi (Win, x86)
Perl program
� Perl學習手札� Perl 學習手札全文
What is “Perl”?
� Perl is an acronym that stands forPractical 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
The end