2010年生命科學現(xiàn)代研究技術(shù)系列講座 -- 數(shù)據(jù)庫與數(shù)據(jù)分析

1、生物信息學課程-- 數(shù)據(jù)庫與網(wǎng)絡(luò)服務(wù),杜舟生物信息學2007級蘇震實驗室,,博二的老人了,Concepts,BioinformaticsComputational BiologyDatabaseWeb serverWeb service,(Many who draw a distinction between bioinformatics and computational biology portray the f

2、ormer as a tool kit and the latter as science. ),Nucleic Acids Research Database and Web Server issue,Database,Web Server,http://www.oxfordjournals.org/nar/database/c/,Database,http://bioinformatics.ca/links_directory/

3、,Web sever,Google !!!,Bioinformatics主要期刊,專業(yè)期刊（以計算文章為主）：Bioinformaitcs,plos computational biology, BMC bioinformatics, journal of computational biology, BMC genomics , BMC systems&

4、#160;biology, molecular biology eolution...準專業(yè)期刊（基本上每期都有一定比例）：genome biology, nucleic acids research, genome research, molecular systems biology, america

5、n journal of human genetics,...  綜合期刊：nature,science,pnas,plos one,...其它（偶爾有計算類文章發(fā)表）：nature biotechnology, nature genetics, nature methods, cell，trends&

6、#160;genetics, plos genetics,...,Part I Overview of the bioinformaticsDatabase and web serverPart II Introduction to bioinformatics webservices created in Su Zhen's labPart III Construction of databas

7、e and web services,,,,,,,,,14,Three major public DNA databases,In 1988, 由此三家組成了國際核酸序列數(shù)據(jù)庫協(xié)作組織（INSDC），規(guī)定：1、數(shù)據(jù)交換與共享（每24小時進行一次）2、使用統(tǒng)一的數(shù)據(jù)記錄格式處理提交數(shù)據(jù)，以保證各數(shù)據(jù)庫相應(yīng)記錄在內(nèi)容上的一致性。3、數(shù)據(jù)的維護與更新。Each database updates only the records that

8、 were directly submitted to it.,,,,,,,,,19,Accession number 是用來確定一個記錄的標簽。Examples (all for retinol-binding protein, RBP4):X02775GenBank genomic DNA sequence（1+5，2+6）NT_030059Genomic contig in RefSeqRs7079946dbS

9、NP (single nucleotide polymorphism)N91759.1An expressed sequence tag (1 of 170)NM_006744RefSeq DNA sequence (from a transcript)NP_007635RefSeq proteinAAC02945GenBank proteinQ28369SwissProt protein1KT7Prot

10、ein Data Bank structure record,protein,DNA,RNA,What is accession number?,20,Accession number series in RefSeq,Experimentally determined sequences NT_123456 Genomic contigs (DNA) NM_123456 mRNA

11、 NP_123456 ProteinsSequences derived through genome annotation efforts XM_123456 Model mRNAs XP_123456 Model proteins,NCBI簡介,NCBI(National Center for Biotechnology Information),建立于1988年主要任務(wù)

12、開發(fā)數(shù)據(jù)庫進行計算生物學研究開發(fā)基因組數(shù)據(jù)分析的工具發(fā)布生物醫(yī)學信息等對于數(shù)據(jù)庫管理數(shù)據(jù)庫GenbankUnigeneRefseqdbSNPdbESTOMIM提供Entrez數(shù)據(jù)庫檢索BLAST數(shù)據(jù)庫序列搜索比對等,利用NCBI獲取所有玉米的全長cDNA,,1.利用關(guān)鍵字 FLI-CDNA搜索2. 選擇nucleotide,,3. 選擇物種 --- 玉米,4.選擇瀏覽方式 （可選）,,,5. 選擇下載方式，可

13、直接下載fasta文件,,,,,,,,Pfam,http://pfam.janelia.org/,,,,,Genome Browser,瀏覽基因組信息：原始測序序列、基因結(jié)構(gòu)、EST支持、轉(zhuǎn)錄因子、序列保守性、SNP等一系列信息。缺點：只適合手工瀏覽，不適和大規(guī)模處理,Jbrowser,UCSC Introduction,University of California Santa Cruz (UCSC)Genome Browser

14、 DatabaseURL：http://genome.ucsc.edu/數(shù)據(jù)構(gòu)成：基因組數(shù)據(jù)基因組間的比對信息參考序列（mRNA, EST）基因注釋信息（ENCODE項目）,UCSC HomePage,,Genome Browser,Customized UCSC Browser,,,蘇震實驗室數(shù)據(jù)庫及網(wǎng)絡(luò)服務(wù)介紹,植物mRNA數(shù)據(jù)庫,Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong

15、 Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, and Zhen Su Nucleic Acids Research, 2010, Vol. 38, Database issue D806-D813,大豆功能數(shù)據(jù)庫,苜蓿數(shù)據(jù)庫,Li D, Su Z, Dong J, Wang T. An expression database for roots of the model legume

16、 Medicago truncatula under salt stress. BMC Genomics. 2009 Nov 11;10(1):517.,植物分泌蛋白數(shù)據(jù)庫,Zhou Du, Xin Zhou, Li Li, Zhen Su, plantsUPS: a database of plants' Ubiquitin Proteasome System, BMC Genomics, 2009, 10:227,植物泛素化

17、系統(tǒng)數(shù)據(jù)庫,玉米信號轉(zhuǎn)導數(shù)據(jù)庫,BMC genomics, 2010,EasyGO：GO富集分析平臺,Xin Zhou, Zhen Su, EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species, BMC Genomics 2007, 8:246,agriGO：農(nóng)業(yè)物種GO富集分析平臺,Z

18、hou Du, Xin Zhou, Yi Ling, Zhenhai Zhang and Zhen SuNucleic Acids Research, 2010Faculty of 1000 biology “Recommend”,,,構(gòu)建數(shù)據(jù)庫或網(wǎng)絡(luò)服務(wù)可能需要用到的技術(shù),Database,,Biological Meaning,Computertechnique,,Linux,Apache,MySQL,PHP/Python/