Bioinformatics
生物資訊學
Bioinformatics (生物資訊學)
生物資訊學
(Bioinformatics)
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What is Bioinformatics?
何謂生物資訊學？
Molecular Biology Review
分子生物回顧
Bioinformatics Web Sites, Servers, and Databases
生物資訊學網站、伺服器、資料庫
Structure and Function of DNA, RNA, and Protein
核酸和蛋白質的結構和功能
Sequence Searching with BLAST
使用BLAST進行序列找尋
Pairwise Sequence Comparison and Alignment
序列的並排比對
Sequence Similarity Searching and Matching
序列相似性找尋與比對
Protein Structure Display and Manipulation
蛋白質的結構展示與操作
Multiple Sequence Alignment多重序列定位排比
Protein Sequence Motifs and Patterns
蛋白質序列功能點與式樣
Hidden Markov Models: Finding Remote Homologs
找尋遠距離之相似物
Introduction to Genomics 基因體導論
Human Genome Web Sites and Servers人類基因體網站
DNA Informatics DNA核酸資訊學
Structural Genomics 結構基因體學
Complete Genomic DNA Sequences完整之基因體核酸序列
Predicting 2D Structure of Protein and RNA 推估之蛋白質和RNA之二維結構
Predicting 3D Structures of Proteins推估之蛋白質之三維結構
Functional Genomics 功能基因體學
High Throughput Biology and Molecular Microarrays 高效能生物學和分子晶片
Molecular Phylogenetics 分子血緣系統學
Molecular Clocks分子時鐘
PCR and Primer Design
PCR和引子設計
Human Genes and Genome 人類的基因和基因體
Genome Sequencing Projects基因體研究計畫
Complete Human Genome Sequence完整之人類基因體序列
Human Genome and Mapping人類基因體和圖譜
DNA Web Sites and Servers核酸網站和伺服器
Unix, PERL, and Database Architecture 資料庫結構
Source (資訊來源):
Info cited on 2019-06-25-WD2 (資訊引用於 中華民國108年6月25日) by 湯偉晉
(WeiJin Tang)
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何謂生物資訊學？
What is Bioinformatics?
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These teaching materials were developed by Dr. R. L. Bernstein of San Francisco State University while on sabbatical at SWBIC and will be presented in his bioinformatics course at SFSU. The contents are translated into Chinese and linked directly to the original web sites. I thank for the permission to use these materials by Dr. R.L. Bernstein (http://www.swbic.org/education/bioinfo/biointro.html ).
 生物資訊學特點
Study of biological information 生物資訊的研究
Interface of biology and computers 生物和電腦的界面
Computational molecular biology 計算分子生物學
Includes genomics 包含基因體學
Subfields: DNA informatics, protein informatics, proteomics
次領域︰DNA資訊學、蛋白質資訊學、蛋白體學
Person is “bioinformaticist”
Sometimes “bioinformatician,” “bioinformatist”
工作者稱為︰生物資訊學家、生物資訊人、生物資訊者
生物資訊學定義
A narrower definition嚴謹定義:
The use of computer tools to store, access, and analyze nucleic acid and amino acid sequence data and protein structural data.
應用電腦工具貯存、採用、分析核酸和胺基酸序列數據和蛋白質結構數據
A broader definition寬鬆定義:
The use of computer tools to store, access, and analyze all types of biological data, including text data, phylogenetic trees, metabolic maps.
應用電腦工具貯存、採用、分析所有的生物數據，包含文字數據、血緣分類樹、代謝圖等
Many applications in biological research, drug design, medicine.
許多應用在生物學的研究、藥物的設計和醫學上。
Bioinformatics Allied 協同領域
Biotechnology 生物技術學
Computer simulations in biology 生物的電腦模擬
Genetics, biochemistry, cell biology 遺傳學、生化、細胞學
Structural biology 結構生物學
Phylogenetics and taxonomy 血緣分類學和分類學
Quantitative biology, mathematical biology, theoretical biology
數量生物學、數學生物學、理論生物學
Epidemiology 流行病學
Medical informatics 醫學資訊學
Drug design 藥物設計
A Bit of History 簡史
First protein amino acid sequence databases in mid-1960’s.
第一個蛋白質序列資料庫在1960年代中期。
Researchers developing algorithms to analyze these data for individual research projects in the 1960’s and 1970’s.
在60和70年代中，研究者發展數學模式分析個別研究計畫的數據
GenBank and other public databases with freely available analysis tools in the 1980’s.
在80年代，基因銀行（美國的基因資訊資料庫）和其他公共的資料庫提供免費的分析工具。
Enormous growth of GenBank and PDB in 1990’s.
在90年代 GenBank和PDB非常巨量的成長
Recent Trends in Research 最新研究趨向
A great surge in genomics: The Human Genome Project
偉大的研究浪潮︰人類基因體計畫
Genome projects for ~400 organisms
約400種生物的基因體計畫
>70 completed published genomes (including chromosomes of higher eukaryotes)
超過70種生物的基因體分析已經完成（包括高等真核生物的染色體）
Recent advances in molecular genetics technologies, especially microarrays.
最新的分子遺傳技術的發展，特別是 microarrays晶片
Push to analyze genes and gene products, and to determine protein structure/function relationships.
推進基因和基因產品的分析、決定蛋白質的結構和功能的關係
Data Explosion 資訊爆炸
These research trends, especially the sequencing projects, have resulted in huge amounts of raw data that must be stored, manipulated, and analyzed.
研究的潮流，特別是序列分析的計畫，獲得了大量的原始數據，這需要貯存、處理和分析。
Computer information technology has also advanced very rapidly and has provided the means for handling this data explosion.
電腦資訊的技術快速地增進，使得有辦法可以處理這些數據爆炸。
Bioinfo Tools & Services 生物資訊學的工具和服務
Databases: text, sequence, structure
資料庫︰文字、序列、結構等資料
Database annotation text searches
資料庫文字註解的找尋
Sequence similarity search tools
序列相似性尋找工具
Sequence and structure analysis tools
序列和結構分析工具
3D structure analysis, visualization tools
立體結構分析、顯像工具
Structure prediction tools
結構預測工具
Phylogenetic analysis tools
血緣分類分析工具
Metabolic analysis tools
代謝分析工具
Comprehensive Servers 完整的伺服器
NCBI - The National Center for Biotechnology Information
美國國家生物技術資訊中心
EMBL - The European Molecular Biology Laboratory
歐洲分子生物實驗室
ExPASy, at Swiss Institute of Bioinformatics
瑞士生物資訊研究所
BCM Search Launcher, at Baylor College of Medicine
PDB: Protein Data Bank
蛋白質機料庫
SCOP: Structural Classification of Proteins
蛋白質結構分類
NCBI Web site: http://ncbi.nlm.nih.gov
New Biology? 新的生物學？Flow of Genetic Information基因資訊的流動
DNA, to RNA (messenger), to protein
Natural process in all cells
所有細胞中天然的過程
Explains how genotype (DNA) creates phenotype (protein) of organisms.
解釋基因型如何創造表現型
DNA bp sequence of each gene, expressed into aa-sequence of unique protein.
基因DNA核酸的序列表現成獨特的胺基酸序列
“Horizontal” transmission of genetic info
遺傳資訊的水平轉移
Regulation of gene expression
基因表現的調控
Transmission of Genetic Information
Flow of Genetic Information 遺傳訊息的傳遞
DNA (chromosome) replicates DNA.
染色體核酸複製核酸
Natural process in all cells
所有細胞中天然的過程
Explains how genotype (DNA) is passed on to daughter cells.
解釋基因型如何傳遞到子代
DNA bp sequence of parent dsDNA, makes two dsDNA product molecules.
親代雙股DNA序列製造出雙股的核酸分子
“Vertical” transmission of genetic info
垂直的遺傳訊息轉移
Transmission of Genetic Information遺傳訊息的轉移
In all forms of life, including viruses..
在所有形式的生命中發生，包括病毒
Cellular apparatus is extensive.
在細胞內的設施很普遍
Protein synthesis is major process in cells.
在細胞內蛋白質合成是主要的過程
Many different proteins in each cell.
在細胞內有許多不同的蛋白質
Proteins determine differentiated properties.
蛋白質決定分化的特性
Bioinformatics identifies genes and proteins, often from DNA sequence only.
生物資訊學確認基因和蛋白質，常從只有核酸序列中得知
Structural Genomics 結構基因體學
Genetic maps: locations of genes
基因圖譜︰基因所在的位置
Physical maps: eg. restriction sites
物理圖譜︰舉例而言限制脢的切點
DNA sequence: ultimate map
DNA核酸序列︰終極圖譜
Major genomics projects主要的基因體計畫
dsDNA represented as ssDNA in databases
雙股DNA在資料庫中是以單股表達
“forward” and “reverse” strands
"前進” 和 “回返” 股
“plus” and “minus” strands, +/-
“Watson” and “Crick” strands
Absolutely complementary to each other.
都是絕對彼此互補的
Genome Example: Helicobacter pylori
基因體舉例︰幽門桿菌
Helicobacter pylori , the ulcer bug 幽門桿菌-潰瘍蠹蟲
Causes ulcers, also gastric cancer 導致潰瘍，含有胃癌
Complete genome: 1.6 Mb of DNA 整個基因體︰ 1.6 Mb
Circular chromosome, about 1600 genes 環型染色體，約1600基因
Genes for pathogenicity, genes for detection by PCR, genes as targets
of drugs, genes for synthetic vaccines
致病性基因、使用PCR偵測的基因、藥物目標的基因、合成疫苗的基因等
Two different isolates sequenced, one by drug company.
兩種不同菌株序列分析，一種為藥廠者
Recently Completed Genomes of Pathogens
最近完成的病原菌基因體
Mycobacterium tuberculosis: tuberculosis肺結核
Neisseria meningitidis: bacterial meningitis 腦膜炎菌
Treponema pallidum: syphilis 梅毒菌
Campylobacter jejuni: foodborne illness 彎曲桿菌-食品中毒菌
Listeria monocytogenes: foodborne gastroenteritis 李斯特單胞菌
Vibrio cholerae: cholera 霍亂菌
Streptococcus pneumoniae: pneumonia 肺炎菌
from Dr. R.L. Bernstein http://www.swbic.org/education/bioinfo/biointro.html
Web Sites for Microbial Genomes
微生物基因體網站
Bioinformatics 範圍
Genomics Areas of Interest 基因體研究興趣範圍
Genome Sizes 基因體大小
Functional Genomics 功能性基因體
DNA Microarrays
from Dr. R.L. Bernstein http://www.swbic.org/education/bioinfo/biointro.html
Summary 結論
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