bioinf03bioinf03

1、生物信息软件综合实践第三章关键词或词组为基础的数据库检索检索数据库的方法u 用关键词或词组进行数据库检索(Text-based database searching)Gene name AuthorAccession numberu 用核苷酸或蛋白质序列进行数据库检索(Sequence-based database searching)Database关键词或词组为基础的数据库检索名词、描述性词、词组序列注册号 (Accession number)关键词最准确可靠NCBI Entrez EBI searchIntegrated database retrieval system (DBGET)

2、检索体系检索须知（1）连接词AND, OR, NOT（Boolean operators）urice AND enzyme(AND为缺省值，可略去)rice AND enzyme NOT kinase retrotransposon OR retroelement注意事项：1、AND, OR, NOT must be entered in UPPERCASE2、Boolean operators are processed in a left-to-right sequence 3、The order can be changed by enclosing individualconcepts

3、 in parentheses (processed first)rice AND retrotransposon OR retroelement9783 recordsPubMedrice AND (retrotransposon OR retroelement)352 records检索须知（2）u 用引号将两个单词组成一个词组16S rRNA = 16S AND rRNA “16S rRNA”exact match16S rRNA3300000 sequencesNucleotide“16S rRNA”380000 sequencesu wild card, *, 放在单词后使检索范围扩

4、大，但专一性降低pseudopod* =pseudopod OR pseudopodia OR pseudopodiumu 表示范围, :, 连接前后关键词，限定范围110:500Sequence Length 2009/3/1:2009/9/30Publication Date1.Entrez/search/NCBI 的检索体系优点：三种检索体系中最容易操作的体系，帮助文档完备Entrez HelpEntrez可对6大类37个数据库进行检索/search/Entrez可对6大类37个数

5、据库进行检索针对基因组已测序完成的物种针对17个广泛研究的模式生物Prokaryotic, chloroplast, mitochondrial, virus, protist, plant针对GenBank中具有大于7万条EST的物种检索方法（1）：跨库检索(cross-database search)Entrez系统中数据库之间的连接NCBI主页选择“All Databases”或Entrez主 页，输入关键词各个数据库中检索到的信息数量点击相应数据库查看信息目录， 每一条信息与其它数据库的相关信息链接检索方法（2）：选择数据库检索NCBI主页选择数据库，输入关键词检索到的信息目录，每一条

6、信息与其它数据库的相关信息链接查看信息内容序列数据库的搜索精简搜索结果查询insulin基因的序列不是想要的结果！如何精简？精简搜索结果的方法1-使用Advanced search查询人（human）的insulin基因的序列关键词查询范围: insulin title human organism如何定义查询范围？任意搜索范围：Xa21All Fields1000:2000Sequence Lengthbiomol_genomicProperties biomol_mrna: mRNA biomol crna: cRNAgbdiv_plnPropertiesModification Date

7、Title注意：关键词和字段名（field）均不区分大小写LOCUSDQ1764241980 bpDNAlinearPLN 12-MAR-2006DEFINITIONOryza sativa (indica cultivar-group) pathogen-induced defense- responsive protein 8 (DR8) gene, complete cds.ACCESSIONDQ176424AccessionGIVERSIONDQ176424.1GI:73918052KEYWORDSHTG.Keyword: EST GSS HTG HTC TPA TSASOURCEOr

8、yza sativa Indica Group ORGANISMOryza sativa Indica GroupEukaryota; Viridiplantae; Streptophyta; Embryophyta;Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade;Ehrhartoideae; Oryzeae; Oryza.REFERENCE1(bases 1 to 1980)AuthorAUTHORSWang,G., Ding,X., Yuan,M., Qiu,D., Li,

9、X., Xu,C. and Wang,S.TITLEDual function of rice OsDR8 gene in disease resistance and thiamine accumulationJournalJOURNALPlant Mol. Biol. 60 (3), 437-449 (2006)PUBMED16514565OrganismPublication Date： 记录公开日期如何定义查询范围？第四章讲述使用序列进行检索FEATURESLocation/Qualifiers source1.646/organism=Dicathais orbita/organel

10、le=mitochondriongene_in_mitochondrionProperties/mol_type=mRNAFeature Key: promoter,/db_xref=taxon:69583mRNA, CDS, exon, intron,/clone=20006E09polyA_signal/note=mitochondrial and ribosomal sequences produced bysuppressive subtractive hybridizationCDS646COXIGene Name/gene=COXI/codon_start=1/transl_tab

11、le=5/product=cytochrome oxidase subunit I/protein_id=ACT34372.1/db_xref=GI:253740054/translation=GTLYILFGMWSGLVGTALSLLIRAELGQPGALLGDDQLYNVIVT AHAFVMIFFLVMPMMIGGFGNWLVPLMLGAPDMAFPRLNNMSFWLLPPALLLLLSSAAORIGIN1 ggtacattat atattctgtt tggaatatga tcaggcctag tgggaactgc tttaagttta61 cttattcgag ctgagttagg ac

12、aacctggg gccctattag gggatgatca attatataat121 gttattgtta cagcacacgc ttttgtaata atttttttct tagttatacc tataatgatc精简搜索结果不同数据库的Search fields不同，详见Limits/Advanced选项！Aim: Find all human nucleotide sequences with the poly(A) signal.polyA_signal“FKEY AND humanORGNAim: Find all human protein sequences with len

13、gths between 50 and 60 amino acids that were entered into the database during 1999.humanORGN AND 50SLEN:60SLEN AND 1999MDATAim: Find Drosophila population studies published in the Journal of Molecular Evolutionj mol evolJOUR AND drosophilaORGNSearch Field Descriptions for Sequence Database精简搜索结果的方法2

14、：直接输入搜索字段查询人insulin基因的RefSeq序列自动将俗名转换为学名精简搜索结果的方法3：组合多次搜索结果查询人insulin基因的RefSeq序列使用Clipboard临时收集多条序列永久保存收集的序列需要注册，然后Send to Collections文献数据库Pubmed的搜索/PubMed/u 美国国家医学图书馆的数据库u 数据来源 MEDLINE：已经规范处理的数据，已标注MeSH Terms，记录标有pubmed-indexed for medline In Process Citations：尚未经规范处理的数据，记

15、录标有pubmed-in process Publisher-Supplied Citations：由出版商提供的电子文献，记录标有PubMed-as supplied by Publisher 搜索结果举例Pubmed自动将检索词翻译为MeSH词汇使用MeSH词汇能获得更加全面、准确的结果12精简PubMed搜索结果的方法：使用AdvancedPubMed数据库的搜索huazhong agricultural universityAffiliation精简PubMed搜索结果的方法：组合多个搜索字段Watson J author 1953 publication date nature jo

16、urnalWatson J AU 1953 DP nature TAPubMed数据库的字段：Search Field Descriptions and Tags for PubmedAffiliation AD Article Identifier AID All Fields ALL Author AUBook book Comment Corrections Corporate Author CN Create Date CRDTCompletion Date DCOM EC/RN Number RN Editor EDEntrez Date EDAT Filter FILTERFirs

17、t Author Name 1AU Full Author Name FAU Full Investigator Name FIR Grant Number GRInvestigator IRISBN ISBNIssue IP Journal TA Language LALast Author LASTAU Location ID LID MeSH Date MHDAMeSH Major Topic MAJR MeSH Subheadings SH MeSH Terms MH Modification Date LR NLM Unique ID JID Other Term OTOwner P

18、agination PGPersonal Name as Subject PSPharmacological Action PA Place of Publication PL PMID PMIDPublisher PUBN Publication Date DP Publication Type PT Secondary Source ID SI Subset SBSupplementary ConceptNM Text Words TWTitle TI Title/Abstract TIABTransliterated Title TT UID PMIDVersion Volume VI如果已知文献部分信息：单篇文献匹配器（Single Citation Matcher）：/pubmed/citmatch多篇文献匹配器（Batch Citation Matcher）：/pubmed/batchcitmatch如何自动获得最近更新的结果？Google学术搜索/schhp?hl=zh-CN检索、管理和引用文献的工具h