生物信息學(xué)分析技巧

數(shù)據(jù)庫(kù)的相似序列搜索

軍事醫(yī)學(xué)科學(xué)院放射與輻射醫(yī)學(xué)研究所李稚鋒

2008.3.19生物信息學(xué)分析技巧數(shù)據(jù)庫(kù)相似性分析需求確定新基因特異引物和通用引物設(shè)計(jì)新基因的功能研究進(jìn)化分析內(nèi)容提綱基本知識(shí)核酸相似性分析編碼序列非編碼序列基因組蛋白質(zhì)相似性分析序列結(jié)構(gòu)域

第一部分：基本知識(shí)生物信息學(xué)生物信息學(xué)(Bioinformatics)是在數(shù)學(xué)、計(jì)算機(jī)科學(xué)和生命科學(xué)的基礎(chǔ)上形成的一門(mén)新型的交叉學(xué)科，它是為理解各種數(shù)據(jù)的生物學(xué)意義，運(yùn)用數(shù)學(xué)、計(jì)算機(jī)科學(xué)與生物學(xué)手段進(jìn)行生物信息的收集、加工、存儲(chǔ)、傳播、分析與解析的科學(xué)常用生物信息資源NCBI

http:///EBI

http://www.ebi.ac.uk/

UCSCGenomeBrowserhttp:///TRANSFAC/http://www.gene-regulation.de/KEGGhttp://www.genome.jp/kegg/GO

/DIP

/NCBIhttp:///DatabasesattheEBIEMBLNucleotideDatabase-Europe’sprimarycollectionofnucleotidesequencesismaintainedincollaborationwithGenbank(USA)andDDBJ(Japan)Ensembl-Providinguptodatecompletedmetazoicgenomesandthebestpossibleautomaticannotation.UniProt–(UniversalProteinResource)istheworld'smostcomprehensivecatalogueofinformationonproteins.ItisacentralrepositoryofproteinsequenceandfunctioncreatedbyjoiningtheinformationcontainedinUniProtKB/Swiss-Prot,UniProtKB/TrEMBL,andPIR.TheUniProtKnowledgebase(UniProtKB)TheUniProtReferenceClusters(UniRef)TheUniProtArchive(UniParc)TheUniProt

MetagenomicandEnvironmentalSequences(UniMES)InterPro-InterProisadatabaseofproteinfamilies,domains,repeatsandsitesinwhichidentifiablefeaturesfoundinknownproteinscanbeappliedtonewproteinsequences.GOA-GeneOntologyAnnotationDatabase.GOAhasbeenamemberoftheGOConsortiumsince2001.TheGOAprojectaimstoprovidehigh-qualityGeneOntology(GO)annotationstoproteinsintheUniProtKnowledgebase(UniProtKB)andInternationalProteinIndex(IPI)andisacentraldatasetforothermajormulti-speciesdatabases;suchasEnsemblandNCBI.MacromolecularStructureDatabase-EuropeanProjectforthemanagementanddistributionofdataonmacromolecularstructuresArrayExpress-forgeneexpressiondataIntAct-Providesafreelyavailable,opensourcedatabasesystemandanalysistoolsforproteininteractiondata.序列格式帶注釋的文本格式GenBank數(shù)據(jù)庫(kù)的序列格式EMBL數(shù)據(jù)庫(kù)的序列格式fasta序列格式核酸序列基序格式蛋白序列功能域格式LOCUSNM_0212571885bpmRNAlinearPRI10-FEB-2008DEFINITIONHomosapiensneuroglobin(NGB),mRNA.ACCESSIONNM_021257XM_001129381XM_001132327VERSIONNM_021257.3GI:61676205KEYWORDS.SOURCEHomosapiens(human)ORGANISMHomosapiens

Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;

Mammalia;Eutheria;Euarchontoglires;Primates;Haplorrhini;

Catarrhini;Hominidae;Homo.REFERENCE1(bases1to1885)AUTHORSNicolis,S.,Monzani,E.,Ciaccio,C.,Ascenzi,P.,Moens,L.and

Casella,L.TITLEReactivityandendogenousmodificationbynitriteandhydrogenperoxide:doeshumanneuroglobinactonlyasascavenger?JOURNALBiochem.J.407(1),89-99(2007)PUBMED17600531REMARKGeneRIF:ferric-NGBactsnotonlyasscavengeroftoxicspecies,butalsoasatargetoftheself-generatedreactivespeciesREFERENCE2(bases1to1885)……COMMENTREVIEWEDREFSEQ:ThisrecordhasbeencuratedbyNCBIstaff.ThereferencesequencewasderivedfromAF422797.1andBC032509.1.OnorbeforeSep25,2007thissequenceversionreplacedgi:113424669,gi:113424936,gi:21361878.

Summary:Thisgeneencodesanoxygen-bindingproteinthatisdistantlyrelatedtomembersoftheglobingenefamily.Itishighlyconservedamongothervertebrates.Itisexpressedinthecentralandperipheralnervoussystemwhereitmaybeinvolvedinincreasingoxygenavailabilityandprovidingprotectionunderhypoxic/ischemicconditions.

PublicationNote:ThisRefSeqrecordincludesasubsetofthepublicationsthatareavailableforthisgene.Pleaseseethe

EntrezGenerecordtoaccessadditionalpublications.COMPLETENESS:fulllength.PRIMARYREFSEQ_SPANPRIMARY_IDENTIFIERPRIMARY_SPANCOMP1-1641AF422797.11-16411642-1885BC032509.11349-1592FEATURESLocation/Qualifierssource1..1885/organism="Homosapiens"/mol_type="mRNA"/db_xref="taxon:9606"/chromosome="14"/map="14q24.3"gene1..1885/gene="NGB"/note="neuroglobin"/db_xref="GeneID:58157"/db_xref="HGNC:14077"/db_xref="HPRD:05602"/db_xref="MIM:605304"

exon1..464/gene="NGB"/inference="alignment:Splign"/number=1CDS376..831/gene="NGB"/codon_start=1/product="neuroglobin"/protein_id="NP_067080.1"/db_xref="GI:10864065"/db_xref="CCDS:CCDS9856.1"/db_xref="GeneID:58157"/db_xref="HGNC:14077"/db_xref="HPRD:05602"/db_xref="MIM:605304"/translation="MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAVVQAMSRGWDGE"

exon465..576/gene="NGB"/inference="alignment:Splign"/number=2

exon577..696/gene="NGB"/inference="alignment:Splign"/number=3

exon697..1876/gene="NGB"/inference="alignment:Splign"/number=4STS1623..1775/gene="NGB"/standard_name="D14S693E"/db_xref="UniSTS:151573"

polyA_signal1857..1862/gene="NGB"

polyA_site1876/gene="NGB"/experiment="experimentalevidence,noadditionaldetailsrecorded"ORIGIN1ttcccaggcc

accatagcgg

ctggcggagg

gagcgcgcgc

cttgctggcc

tggagggggc61gggggccgtg

gcggctttaa

agcgcccagc

ccaggcgtcg

cggggtgggg

cggctctggc121ggctgcgggg

cgcagggcgc

agcggccaag

cggggtcccc

ggaagcacag

ctggggtgtc181tccacctacg

actggccgcg

cgccttttct

ctcccgcgcc

agggaaggag

cggctgcggc241ccccgccggg

cggaggcacg

gggggcgtac

gaggggcgga

ggggaccgcg

tcgcggagga……1741gtactcaggc

agctggagag

aagagaaggc

agcagcagag

gcccccgccc

tcaccccagc1801catctgcact

tgtaccattt

gctctgtgct

gactgtggtc

ctataaattc

atgagaaata1861aactggttct

gtgtgcaaaa

aaaaa//GenBank數(shù)據(jù)庫(kù)的序列格式IDUPHOXE13standard;DNA;HUM;133BP.XXACM60941;XXSVM60941.1XXDT10-APR-1991(Rel.28,Created)DT18-JAN-1995(Rel.42,Lastupdated,Version4)XXDEHumanmicrobicidaloxidase(p47-phox)gene,exon1andpartialcds.XXKWautosomalchronicgranulomatousdiseaseprotein;microbicidaloxidase;KWNADPHoxidase.XXOSHomosapiens(human)OCEukaryota;Metazoa;Chordata;Craniata;Vertebrata;Mammalia;Eutheria;OCPrimates;Catarrhini;Hominidae;Homo.XXRN[1]RP1-133RXMEDLINE;91187870.RACasimirC.M.,Bu-GhanimH.N.,RodawayA.R.,BentleyD.L.,RoweP.,RASegalA.W.;RT"AutosomalrecessivechronicgranulomatousdiseasecausedbydeletionataRTdinucleotiderepeat";RLProc.Natl.Acad.Sci.U.S.A.88:2753-2757(1991).XXEMBL數(shù)據(jù)庫(kù)的序列格式常染色體隱性肉芽腫性疾患CCNCBIgi:189948XXFHKeyLocation/QualifiersFHFTsource1..133FT/db_xref="taxon:9606"FT/sequenced_mol="DNA"FT/organism="Homosapiens"FT/tissue_type="blood"FTCDS<1..33FT/codon_start=1FT/note="NCBIgi:189949"FT/gene="CYBB"FT/map="Xp21.1"FT/product="microbicidal

oxidase"FT/protein_id="AAA60086.1"FT/translation="FEKRFVPSQHY"FTintron34..>133FT/note="G00-120-513"FT/gene="CYBB"FT/map="Xp21.1"XXSQSequence133BP;30A;37C;45G;21T;0other;

tttgagaagc

gcttcgtacc

cagccagcac

tatgtgagta

gctggtggag

ggcatcccgt60

ggggggaata

cgggagggac

agcacggcca

cccttgcagt

cccagggcca

accagctcca120

gtgaggacta

acg133//EMBL數(shù)據(jù)庫(kù)的序列格式核酸序列FASTA格式多條核酸序列的FASTA格式>gi|10639033|emb|AJ245946.1|HSA245946HomosapiensmRNAforneuroglobin(NGBgene)ATGGAGCGCCCGGAGCCCGAGCTGATCCGGCAGAGCTGGCGGGCAGTGAGCCGCAGCCCGCTGGAGCACGGCACCGTCCTGTTTGCCAGGCTGTTTGCCCTGGAGCCTGACCTGCTGCCCCTCTTCCAGTACAACTGCCGCCAGTTCTCCAGCCCAGAGGACTGTCTCTCCTCGCCTGAGTTCCTGGACCACATCAGGAAGGTGATGCTCGTGATTGATGCTGCAGTGACCAATGTGGAAGACCTGTCCTCACTGGAGGAGTACCTTGCCAGCCTGGGCAGGAAGCACCGGGCAGTGGGTGTGAAGCTCAGCTCCTTCTCGACAGTGGGTGAGTCTCTGCTCTACATGCTGGAGAAGTGTCTGGGCCCTGCCTTCACACCAGCCACACGGGCTGCCTGGAGCCAACTCTACGGGGCCGTAGTGCAGGCCATGAGTCGAGGCTGGGATGGCGAGTAAGAGGCGACCCCGCCCGGCAGCCCCCATCCATCTGTGTCTGTCTGTTGGCCTGTATCTGTTGT>gi|10639821|emb|AJ245945.1|MMU245945Mus

musculusmRNAforneuroglobin(Ngbgene)GCTGCATGTGCGTTGACTGCACCCACGCCTCGAGGGTCCCATCACTGCGTCCCGCGAGTCTCCTGGGAGAGAGAGCATGGAGCGCCCGGAGTCAGAGCTGATCCGGCAGAGCTGGCGGGTAGTGAGCCGCAGCCCTCTGGAACATGGCACTGTCCTGTTCGCCAGGCTCTTCGCCCTGGAACCCAGCCTGCTGCCTCTCTTCCAGTACAATGGCCGCCAGTTCTCCAGCCCTGAGGACTGTCTCTCCTCTCCAGAATTCCTGGACCACATTAGGAAGGTGATGCTAGTGATTGATGCTGCAGTGACCAACGTGGAGGACCTGTCTTCATTGGAGGAGTACCTGACCAGCTTGGGCAGGAAGCATCGGGCAGTGGGAGTGAGGCTCAGCTCCTTCTCGACAGTAGGCGAGTCCCTGCTCTACATGCTGGAGAAGTGCCTGGGTCCCGACTTTACACCAGCTACAAGGACCGCCTGGAGCCGACTCTACGGAGCTGTGGTGCAAGCCATGAGCCGAGGCTGGGATGGGGAGTAAGAGACGAGCCAGTGCCCCTATCTATGTGTGTCTGTCTGTTGATCTGCCTGTTGTAGTCTTAGCCTCTCCCCCAGGGTCTCTCTATACCTTGGTC蛋白序列FASTA格式單一蛋白質(zhì)序列的FASTA格式>gi|10639034|emb|CAC11133.1|neuroglobin[Homosapiens]MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAVVQAMSRGWDGE相當(dāng)于自由書(shū)寫(xiě)格式>HsNGB,151aaMERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAVVQAMSRGWDGE多條蛋白質(zhì)序列的FASTA格式>gi|10639034|emb|CAC11133.1|neuroglobin[Homosapiens]MERPEPELIRQSWRAVSRSPLEHGTVLFARLFALEPDLLPLFQYNCRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLASLGRKHRAVGVKLSSFSTVGESLLYMLEKCLGPAFTPATRAAWSQLYGAVVQAMSRGWDGE>gi|10639822|emb|CAC11135.1|neuroglobin[Mus

musculus]MERPESELIRQSWRVVSRSPLEHGTVLFARLFALEPSLLPLFQYNGRQFSSPEDCLSSPEFLDHIRKVMLVIDAAVTNVEDLSSLEEYLTSLGRKHRAVGVRLSSFSTVGESLLYMLEKCLGPDFTPATRTAWSRLYGAVVQAMSRGWDGE核酸序列基序格式ALPHABET=ACGTlog-oddsmatrix:alength=4w=9-4.275-0.182-4.1951.408-4.296-1.4871.880-0.816-2.160-1.492-4.1711.474-0.810-4.0761.872-2.1641.537-1.487-4.195-4.2050.1130.340-0.237-0.209-0.4540.9230.390-0.834-1.336-0.0820.9050.1000.674-4.1830.130-0.201log-oddsmatrix:alength=4w=6-2.0320.3241.371-0.781-0.4090.560-0.2500.119-4.274-0.519-0.2601.167-2.1882.300-4.191-2.4651.265-4.111-0.267-2.180-1.9772.158-1.661-2.071蛋白序列功能域格式PatternprofileProfileHMMsavefileformatSELEXMultiplesequencealignmentfileformatPROSITEProfileformat序列分析實(shí)用軟件包EMBOSS-TheEuropeanMolecularBiologyOpenSoftwareSuite/SMS-TheSequenceManipulationSuite/sms2/第二部分：核酸相似性分析編碼序列表達(dá)序列mRNA，CDS，EST多序列比對(duì)NCBIBLASTBLAST-BasicLocalAlignmentSearchTool/blast/Blast.cgi多序列比對(duì)ClustalW

ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalw-2.0.5-win.msi比對(duì)結(jié)果clustal格式*.aln需要GDE格式引物設(shè)計(jì)中的相似性問(wèn)題PrimerPremier軟件特異引物和通用引物特異性檢查PSChttp:///PSC/非編碼序列非編碼基因順式元件非編碼基因序列已有數(shù)據(jù)庫(kù)http://biobases.ibch.poznan.pl/ncRNA/.au/rnadb/miRNAhttp://microrna.sanger.ac.uk/sequences/index.shtmlRNA二級(jí)結(jié)構(gòu)ViennaRNAPackage，mfold二級(jí)結(jié)構(gòu)相似性分析Infernal

http:///按序列和結(jié)構(gòu)相似性預(yù)測(cè)microRNA的工具M(jìn)iRscan，miRAlign，MiRFinderInfernal#STOCKHOLM1.0tRNA1 GCGGAUUUAGCUCAGUUGGG.AGAGCGCCAGACUGAAGAUCUGGAGGUCCtRNA2 UCCGAUAUAGUGUAAC.GGCUAUCACAUCACGCUUUCACCGUGGAGA.CCtRNA3 UCCGUGAUAGUUUAAU.GGUCAGAAUGGGCGCUUGUCGCGUGCCAGA.UCtRNA4 GCUCGUAUGGCGCAGU.GGU.AGCGCAGCAGAUUGCAAAUCUGUUGGUCCtRNA5 GGGCACAUGGCGCAGUUGGU.AGCGCGCUUCCCUUGCAAGGAAGAGGUCA#=GCSS_cons<<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<tRNA1 UGUGUUCGAU