基因相关名词解释

1.High-throughputsequencingHTSSanger,,(nextgenerationsequencingNGS),,(Deepsequencing)2.SangerSangerDNA(dNTP)(ddNTP)ddNTP3-OHGATCdNTPsddNTPsX-3.SNPSNVsinglenucleotidepolymorphismSNPsinglenucleotidevariants,SNVDNA()DNADNA10001somaticmutationSNV4.INDEL(50bpSNP/SNV5.copynumbervariationCNVDNA213A-B-C-DA-B-C-C-D/A-C-B-C-D/A-C-C-B-C-D/A-B-DCA-B-C-C-DA-C-B-C-D6.structurevariationSVCNVinter-chromosometrans-locationSVCircos7.SegmentduplicationSDDNAY22SD8.genotypeandphenotype9.Readreads10.soft-clippedreadsreadsreadsreadssoft-clippedreadsreads11.multi-hitsreadsreadsreadsreadsreads12.FunctuionalgenomicsPostgenomicscDNAmRNAserialanalysisofgeneexpression,SAGEcDNAcDNAmicroarrayDNADNAchipsequencetaggedfragmentsdisplay13.(ComparativeGenomics)14.DNADNAmethylationgenomicimpritingmaternaleffectsgenesilencingRNARNAediting15.1416.()5%17.genomics18.(Genomeannotation),,DNA1.GenomeRe-sequencing2.denovodenovo3.wholeexonsequencingDNASNPIndel4.ChipChip-seqChromatinImmunoprecipitationChIPDNAChIPChIP-SeqDNAChIP-SeqChIPDNADNADNA5.DNADNADNACpG5'CpG1001000bpCpGCpG56CpG288901Mb515CpGMb105CpGCpGDNA6.ScaffolddenovoreadsContigs454Paired-endIlluminaMate-pair3Kb6Kb10Kb20KbContigContigsScaffold7.ScaffoldN50ScaffoldN50ContigN50ContigsScaffoldsScaffoldScaffoldScaffoldsScaffold1Scaffold2Scaffold3...Scaffold25ScaffoldScaffoldScaffoldScaffoldN50Scaffold1+Scaffold2+Scaffold3+Scaffold4+Scaffold5=Scaffold*1/2Scaffold5ScaffoldN50ScaffoldN508.2M10X20MGCGap98%2%9.metagenomicMagenomics1.(1)Metagenomics2.(2)MetagenomicsDNARNA1.mRNARNA-seqtranscriptomicsRNAmRNARNAIlluminamRNAmRNAmRNApoly-ARNAcSNPmRNA2.smallRNASmallRNAmicroRNAssiRNAspiRNAsIlluminaSmallRNA18-30ntSmallRNARNAcDNADNAIlluminaSmallRNAmiRNAmiRNAmiRNAs3.miRNAmicroRNAmiRNA17~24ntRNAmRNAmRNAmicroRNAmicroRNAmicroRNAmicroRNA4.RIP-seqRNAImmunoprecipitationRNAmiRNARNA-RNARIPChIPRNA-DNA-RIPChIPRIPRNARIPRIPmicroarrayRIP-ChipRNA5.CLIP-seqCLIP-seq,HITS-CLIP(crosslinking-immunprecipitationandhigh-throughputsequencing),RNARNARNARNARNARNA-RNART-PCRRNARNA6.(geneexpressionprofile)cDNA,cDNA,cDNAmRNA,,7.ContigreadsoverlapContig8.ContigN50ReadsContigsContigContigContigsContig1Contig2Contig3...Contig25ContigContigContigContigN50Contig1+Contig2+Contig3+Contig4=Contig*1/2Contig4ContigN50ContigN509.RPKMFPKMRPKM,ReadsPerKilobaseofexonmodelperMillionmappedreads,isdefinedinthisway[Mortazavietal.,2008]:1mapreadsmap1Kreads1reads1KreadsRPKMRKPM(exon)=109*exon_tag_count/(total_tag_count*exon_size)RPKM(gene)=109*gene_tag_count/(total_tag_count*canonical_transcript_size)1000000mappedreadskbmappedexonreadreadsreadsmRNA:read1000reads1005kbRPKM10^9*1000(reads)/10^6(reads)*5000()=2001000(reads)/1()*5(K)=200FPKM(fragmentsperkilobaseofexonpermillionfragmentsmapped).FPKMRPKMFPKMfragmentsRPKMreadsFragmentreadFPKMpair-endfragmentread10.1de-novo2de-novooverlapreadscontigscaffoldvelvettrans-ABYSSTrinityreadreadsjunctionscripturecufflinks11.genefusionRSNP1.PCRPCR(Allele-specificPCRAS-PCR)SNP()3SNP()()AS-PCRSNPPCRSNPAS-PCR11(Allele1)2(Allele2)SNP(T-C)P1P21SNP(T)2SNP(C)(1A)1(Genotype1)P1P2P131SNPTP231SNPT1TT2(Genotype2)CC3(Genotype3)TC(1B)SNP(1C)1.AS-PCR2.DHPLC(denaturinghighperformanceliquidchromatographyDHPLC),SSCPDGGESNPDHPLC(TMHA)SNPsPCRDNADNA2DNA122DHPLCDNADNA(meltingpelting)DNA(retentiontime)DNA(acetonitrile)DNA(reverse-phasecolumns)19950efnerWAVEDNA:1.1.PCR2.2.PCR3.3.9550.03/S254.4.DNA5.5.10lPCR3.DGGE&TGGEDGGE(denaturinggradientgelelectrophoresis)DNADNA(temperaturegradientgelelectrophoresis,TGGE)DGGEDNADNATGGE/DGGEDNAG.CA.TG.Clowermeltingdomainhighmeltingdomain(2)DNA3PCR2.3.DNA4.CRS-PCR-RLFPDNAATCGRFLPRFLPCRS-PCR-RFLPCRS-PCR-RFLPcreatedrestrictionsitePCRPCR-RFLP3SNPRFLP:1.CRS-PCR20-25bpCRS-PCR100bp2.2.CRS3.3.3G-AG-GC-CPCR4.4.33PCR5.5.6.6.(single-strandconformationalpolymorphismSSCP)SSCPPCRPCR-SSCP:PCRDNAPCRDNADNADNADNASSCPSNPDNA:1.1.SSCPSSCPSSCPDNADNAssDNADNASSCPDNADNA2.2.DNASSCPDNARNADNARNADNA(400bP)DNASSCP3.3.DNASSCP(4-15)SSCP5min(250V)100VDNA4.4.DNASSCPDNARNASSCPDNA(DNASSCP)WhiteDNADNASSCP92(22%)DNA5.5.SSCPSSCPPAGDNADNA16--18cmDNADNADNA3mm3mmSSCPPCRPAGSSCPSSCP