ACEDBACEDBACEDB( C.elegans 1991 Richard Durbin Jean Thierry-MiegC.elegans Durbin Thierry-Mieg ACEDB [3] ” [4 5] ACEDB 1997 [3] 25-30ACEDB Unix Macintosh OS Windows DNA ,ACEDB ACEDB (throwaway)” ACEDB ACEDBACEDB ACEDB ACEDB ACEDB Sanger (Colorado State University) Aedes aegypti Massachusetts General Arabidopsis Walter Eliza Hall (WEHL)ACEDB Unix X-window World Wide Web Java ACEDB X-window Xace 4,3LMMMRMACEDB ACEDB 13.1 Grain Gene Triticeae ACEDB ACEDB ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oReference LM KeySet Reference reference BCG-28-48713.113.1 reference locus iBgllocus LM reference locusACEDB Sydney BrunoGaeta [7] Cornell Dave.Matthecos [8]ACEDB sequencegene reference 13.2 models.wrm wspec ACEDB [9]ACEDB [10]//this shows partial models for the Sequence,//Locus and Paper class?Sequence DNA UNIQUE ?DNA UNIQUE IntStructure Length UNIQUE IntProperties PseudogeneCDSGenomic_canonicalLocus ?Locus XREF SequencePaper ?PaperRemark Text?Locus Sequence ?Sequence XREF LocusPaper ?Paper?paper Title Textww .d o c u -t r a c k .c w .d o c u -t r a c k .c o13.2 modles.wrmsequence locus paper informationStructure CDS Paper Int ?PaperSequence 13.2 DNA DNA Properities?Sequence Text Float Date Int length 100 one hundred Paper loci remarks UNIQUE sequenceACEDB sequencePaper ?paper?Paper Sequence Paper Link 13.1 Sequence Paper Paper Sequence XREF cross-reference Sequence XREFLocus ?Locus XREF SequenceXREF XREF class ?Locus class-XREFs Int Text Float DateType XREF target tag XREF Locus ?LocusSequence seqenceSequence ?SequenceSequence ?Locus XREF LocusSequence ?Sequence XREF Locus// models.wrm // models.wrmww .d o c u -t r a c k .c w .d o c u -t r a c k .c oACEDB X-windows [12] sequence paper 13.3Genomic_Canonical [13]ACEDB “query be exmple “query builder13.1 KeySetFind Sequence ATHFOO1; Follow LocusFind Sequence AGE>10Sequence AgeACEDB TableMaker TableMaker TableMaker [14-16]Sequence"ATHFOOI"Length 3879Remark " a very strange Arabidopsis thaliana DNA."Locus "FOOI"Genomic_canonicalRemark " a second remark"Locus "FOOI"ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oPaper "smith_1997_aahmt"13.3 ACEDBACEDB FTP Unix FTP FAQ [3] 4.3 ACEDB ACEDB [17]ACEDBACEDB Map Clone GirdFeature Map,Fmap Gene Finder[18] Blixem BLAST[19] [20] DOTTER [21]Fmap C.elegans13.4 Schizosaccharomycespombe rhp61.Locator : a)Zoom InZoom Out Whole b) LM c)MM LM2.Sequence and ends EM 250728sequence3.Summary4.Scale Origin5.Genes “Genes” mRNA CDS6.Features : EMBL GeneBank7.ATGGeneFinderww .d o c u -t r a c k .c w .d o c u -t r a c k .c o8.ORFs9.Gene Finder Coding Sequence10.Coding Frame11.Pssearch PROSITE12.BLASTX maximal segment pairs,MSPs BLAST HSPs BLASTX13.Gene Translation RM Show Translation Color Exons14.BLASTN BLASTN MSPs15.INTRON_HMM16.Gene Finder Splice Site ATG17.DNA Sequence Base ATG RM Color Exon 5’ 3’ Rev-CompLM Rev-Comp RM13.4Sequence Column 13.4 ATG ORFs DNA GeneFinder GeneFinder Coding Segments GeneFinder Splice Site curation BLASTX BLASTN INTRON HMM13.4 CES FmapEfetch BlixemBLASTN BLASTX EfetchAnalyse in Blixem Efetch[22] ACEDB BMBL GeneBank ACEDB ACEDB Fetching Sequence Retrieval System EfetchBlixm[20] BLAST 13.5 S.pombe rhp6 BLASTX BLIXEM MSPs MSPs ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oMSPsLM MSPs MSPs MSPs LM Bliexm Fmap MSPsDOTTER( )BLIXEM DOTTER BLIXEM [20,21] 13.6 S.pombe C8A4.02C SPA C8A4.02C 36 LM25 255 Greyramp 13.6ACEDB DOTTER BLIXEM DNA BLIXEMDNA/DNA BLAST HSPs HSPs BLAST[21]GeneFinderGeneFinder[18] ACEDB ACEDB ACEDB GeneFinderGeneFinder wpf GeneFinderGeneFinderFmap GeneFinder RM GeneFinder Features Fmap wpf Autofind One Gene Fmap temp_geneAutoFind One Gene GeneFinder GeneFinder 3’ 5’ ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oGene->Selected Show Selected 13.1Parameter Assembly GeneFinder 13.2Method GeneFinder Fmap Fmap RM GeneFinder GeneFinder Summary Bar 13.4 temp_gene RM Update Origin13.4 RM Fmap Recalculate GeneFinder Sequence( (write access to)13.1 S.pombe rhp6 Genefinder13.2 GenefinderImporting Sequence Magic TagsFmap Import Sequence RM Fmap aceSequence "MysortSeq"DNA "MyShortSeq"Dna "MyShortSeq"cacacacaccacacccacaccacaccacaccacacccacacccacacacaccacacccacacaccacacccacaccaactctctctcatctacctttactcgcgctgtcacaccttacccggctttctgaccgaaattaaaaaaaatgaaaatgaaatcctgttctttagccctacaacaSequence( DNA Sequence( MyShirSeq Fmap Sequence( DNA Sequence( Sequence MyShirSeqMyShortSeqDNA MyShortSeq 180ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oDNA Int field DNA “Magic Tag” Magic Tag ACEDB Magic Tag [9]GeneBank EMBL ace [23] GeneBank- -ace ace13.7 ACEDB CDS mRNA) GB:ATABIIG Sequence GB:ATABIIG sequence( 81Sequence "LINK_MySeqs"Subsequence "MyShortSeq" 1 180Subsequence "MyShortSeq" 100 20000BLAST MSPcrunchFmap, BLAST, DOTTER BLAST ACEDBBLASTXBLASTN ESTsTBLASTX ESTsBLASTN ESTsBLAST BLAST MSPcrunch MSPcrunch1. BLAST MSPcrunch2. MSPs MSPcrunchMSPs3.MSPcrunch MSPs MSPs4.MSPcrunch BLAST ace1-3 BLAST MSPs MSPcrunch aceBLAST BLAST BLAST E-MAIL MSPcrunch aceww .d o c u -t r a c k .c w .d o c u -t r a c k .c o13.7 GeneBank- -aceACEDB FmapFmap Sequence( “Method( )” Methods( Blixem BLASTN :Method BLASTNColour LIGHTBLUEScore_by_width Score_bounds 100 400Right_priority 5.2BlastnBlixem NMothed( Magic Tag( [9]Homol DNA Homol ?Sequence XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE intPop Homol ?Protein XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE intMotif Homol ?Motif XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE intFeature Method Int Int UNIQUE Float UNIQUE TextHomol Magic Tag( DNA PROSITE 13.4 11BLAST MSPcrunch aceSequence MyShortSeqDNA_homol Z47047 BLASTN 900 1 180 1 180DNA_homol BLASTMSP BLAST MyShortSeq 1-180 900Z47047 1-180 13.4 HiddenMarkov Model 15 “Feature”Magic Tag( aceSequence MyShortSeqFeature INTRON_HMM 100 120 10.12ww .d o c u -t r a c k .c w .d o c u -t r a c k .c oAnalysis (LM) DNA Analysis (DNA DNA KeySetDNA DNA AA ENTER KeySet KeySet DNA Fmap DNA“DNA and amino acid nomenclature” DNA Motif aceMotif "Branch"Match_sequence yTrAyRemark "Splice branch site consensus"Remark "Y is pYrimidine, R is puRine"DNAMotif "HaeI"March_sequence "wGGCCw"Offset 3Cleavage "wGG'CCw"Overhang 0Remark "unpublished observations"DNAMatch_sequence Motif Magic Tag(Branch:HaelKeySet Motif KeySetMax MisMatch(RM) Agarose-gelDump sequence: FASTA Fmap Active Zone(Fmap KeySetww .d o c u -t r a c k .c w .d o c u -t r a c k .c oBLAST Submission: blast_mail ______________________ Fastamail Submission: fastamail_mail ______________________Splice Consensus: 3’ 5’ DNA (DNA Analysis)Codon Usage: KeySetSequence Lengths: KeySet AnalysisData Export: Fmap RM CDS FASTA Active ZoneEMBL Dump: EMBLAcembly ACEDB Acembly ACEDB ABI Uirich Savauge, Danielle, Jean Thierry-MiegAcembly (Unix ACEDBAxembly ACEDBw w.do c u-t r a c k.cw.d o cu-t r a c k.c o。