Master Index
For version 1.5 (2004)
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---bitsize-check-config-csel-exec_notes-fofn-maxdb-maxseq-no_csel-no_exec_notes-no_rawdata_note-no_win-nocheck-nowin-rawdata_note-read_only-win_compact-win_separate
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.assembly/assemble.dat.assembly/assemble_stderr.assembly/cap2_stderr.assembly/cap2_stdout.assembly/cap3_stderr.assembly/cap3_stdout.assembly/constraints.ascii.assembly/constraints.dat.assembly/constraints_stderr.assembly/fofn.assembly/graph.dat.assembly/graph_stderr.assembly/phrap_stderr.assembly/phrap_stdout.assembly/write_exp_file_stderr.assembly/write_exp_file_stdout.aux.blast.cap3_info.con.results.con.contigs.qual.contigs.cvec_failed.cvec_passed.failed.fasta.cat.fasta.masked.log.fasta.masked.fasta.out.xm.fasta.out.fasta.tbl.gaprc.log.passed.phrap_log.pregap4rc.report.scf_dir.screenseq_failed.screenseq_passed.screenvec_failed.screenvec_passed.singlets.svec_failed.svec_passed.tagrep_free.tagrep_log.tagrep_repeat.tk_utilsrc
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2nd-Highest Confidence
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3 Character Amino Acids: contig editor
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64-bit Gap4 databases
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_com
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AC: experiment file line typeActive sequence: spinActive tagsAdding modulesALF/ABI to SCF conversion configurationALF/ABI to SCF conversion moduleAlign sequences: spinAlign: contig editoraligned readings: printingaligned readings: saving to filealigned readings: sorted on alignment scorealigned readings: sorted on alignment scoreAlignment local: spinAlignment matrix fileAlignment scoresallcontigs listallcontigs listAllow del any in cons: contig editorAllow del dash cons: contig editorAllow del in read: contig editorAllow F12 for fast tag deletion: contig editorAllow insert any in cons: contig editorAllow insert in read: contig editorAllow reading shift: contig editorAllow replace in cons: contig editorAllow transpose any: contig editorAllow uppercase: contig editorallreadings listallreadings listAlt left mouse button: overviewalu_onlyAnnotating contigsAnnotating readingsAnnotation SelectorAnnotation structure: doctor databaseAnnotations, searching forAnnotations: contig editorAnnotations: contig editorAnnotations: deleting (Doctor Database)annotations: entering from a fileAnnotations: outputting to file (Doctor Database)AP: experiment file line typeAQ: experiment file line typeArguments, command lineassem_d_thresholdassem_e_rateassem_numberassem_o_thresholdAssemble: independently i.e. ignoring previous dataassembly problems: breaking contigsassembly problems: breaking contigsassembly problems: disassembling readingsassembly problems: disassembling readingsassembly problems: removing readingsassembly problems: removing readingsAssembly: bwa alnAssembly: bwa dbwtswAssembly: CAP2Assembly: CAP3 informationAssembly: CAP3Assembly: directedAssembly: failure codesAssembly: FAKIIAssembly: fasta/fastqAssembly: HuangAssembly: import CAP2Assembly: import CAP3Assembly: import FAKIIAssembly: into new contigsAssembly: into one contigAssembly: into separate contigsAssembly: large projectsAssembly: limitsAssembly: maxdbAssembly: maxseqAssembly: MyersAssembly: perform and import CAP2Assembly: perform and import CAP3Assembly: perform and import FAKIIAssembly: perform CAP2Assembly: perform CAP3Assembly: perform FAKIIAssembly: PhrapAssembly: resetting limitsAssembly: screen onlyAssembly: shotgunAssembly: single stranded regionsAssembly: stack readingsAssembly: stand alone CAP2Assembly: stand alone CAP3Assembly: tg_indexAssembly: tipsAssemblyAssemblyATQA configurationATQA moduleatqa.p4mAugment Experiment files configurationAugment Experiment files moduleAugment, by line typesAugment, by text databaseaugment_exp.p4mAuthor test:spinAuto-diff traces: contig editorAuto-display Traces: contig editorAuto-save: contig editorAV: experiment file line type
b
Backing up databasesband_widthBap databases: conversion to gap4Base accuracies - use ofBase composition plotting:spinBase: SCF structureBASE_BRIEF_FORMAT1BASE_BRIEF_FORMAT1BASE_BRIEF_FORMAT2BASE_BRIEF_FORMAT2Batch modeBC: experiment file line typebit_sizebitsize (command line option)Blast screen configurationBlast screen moduleblast.p4mBreak contig: contig editorBreak contigBreak contigBusy fileBUSY filesButtons: mouse overviewButtonsbwaByte ordering: SCF
c
Calculate consensus: algorithmCalculate consensus: algorithmCalculate consensus: confidenceCalculate consensus: confidenceCalculate consensus: extended consensusCalculate consensus: normal consensusCalculate consensus: normal consensusCalculate consensus: qualityCalculate consensus: reliabilityCalculate consensus: reliabilityCalculate consensus: unfinished consensusCalculate consensusCalculate consensusCap2 assembly configurationCap2 assembly moduleCAP2 assembly: importCAP2 assembly: perform and importCAP2 assembly: performCAP2 assembly: stand aloneCAP2 Assemblycap2_assemble.p4mCap3 assembly configurationCap3 assembly moduleCAP3 assembly: importCAP3 assembly: informationCAP3 assembly: perform and importCAP3 assembly: performCAP3 assembly: stand aloneCAP3 Assemblycap3_assemble.p4mCC: experiment file line typeCF: experiment file line typeCFCH: experiment file line typeChange directoryChanging the default number of matches: spinChanging the maximum number of matches: spinChanging the score matrix: spincheck (command line option)Check assemblyCheck assemblyCheck database: annotation checksCheck database: clone checksCheck database: contig checksCheck database: database checksCheck database: ignoringCheck database: note checksCheck database: reading checksCheck database: template checksCheck database: vector checksCheck databaseCheck databasecheck_paramsChunks, ZTRcircular sequences:spinCL: experiment file line typeClear: in output windowclip_modeClipping by differencesClipping by N basesClipping by quality, ends onlyClipping by qualityclipping readingsClipping within Gap4Clone structure: doctor databaseCloning site, definingCloning site, findingCloning vector clip configuration (old style)Cloning vector clip configurationCloning vector clip module (old style)Cloning vector clip modulecloning_vector_clip.p4mCLOS note typeCloverleaf:spinCN: experiment file line typeCodon composition:spinCodon frequencies:spinCodon tables:spinCodon usage method:spinCodon usage tables:spinCodon usage:spinColour blindnessColour configuration windowColour selectorColour: contig editor highlight disagreementsColour: contig editor highlight disagreementsColoursCommand line arguments: TrevCommand line argumentsCommand line argumentsCommands menu: contig editorComments: SCFComparator windowComparator windowCompare Strands: contig editorComplement contigComplement sequence: spinComponent configurationComponentsComposition: sequence:spinCompress Trace Files configurationCompress Trace Files modulecompress_trace.p4mcompressionCompressions: suggested experimentsconf_valConfidence in contig editorConfidence of base callsConfidence of base callsConfidence of consensusConfidence of consensusConfidence values - use ofConfidence values graphConfidence values: editing techniquesconfiguration files: pregap4Configuration filesConfiguration: pregap4 low levelConfigure menusconfigure: contig editorconfigure: contig editorConfigure: restriction enzymes: spinConfigure: restriction enzymesConfigure: restriction enzymesconfigure_dialogueConfiguring modulesConfiguring pregap4Configuring: fontsConsensus algorith in contig editorConsensus calculation confidenceConsensus calculation confidenceConsensus calculation methodConsensus calculation methodConsensus discrepancies: searching for in contig editorconsensus IUB codesconsensus IUB codesConsensus TraceConsensus: contig editorConsensus: contig editorConsensus: outputtingConsensus: outputtingConserved bases in tRNA:spinConsistency displayContig breakingContig comparator: auto navigationContig comparator: auto navigationContig Comparator: manipulating resultsContig Comparator: manipulating resultsContig comparator: next buttonContig comparator: next buttonContig ComparatorContig ComparatorContig complementingContig Editor: 3 Character Amino AcidsContig Editor: alignContig Editor: alignment coordinatesContig Editor: allow del any in consContig Editor: allow del dash in consContig Editor: Allow del in readContig Editor: Allow F12 for fast tag deletionContig Editor: allow insert any in consContig Editor: allow insert in readContig Editor: allow reading shiftContig Editor: allow replace in consContig Editor: allow transpose anyContig Editor: allow uppercaseContig Editor: annotationsContig Editor: annotationsContig Editor: Auto-diff tracesContig Editor: auto-display tracesContig Editor: auto-saveContig editor: break contigContig Editor: commands menuContig Editor: Compare StrandsContig editor: confidence valuesContig Editor: cursor movementContig Editor: cursorContig Editor: cursorContig Editor: cutoff dataContig Editor: cutoff dataContig Editor: cutoff valuesContig Editor: cutoff valuesContig editor: disassemble readingsContig Editor: Dump ContigContig Editor: edit by base confidenceContig Editor: edit by base typeContig Editor: edit mode setsContig Editor: edit modesContig Editor: editing featuresContig Editor: editing featuresContig Editor: editing keysContig Editor: editing keysContig Editor: editing techniquesContig Editor: group readingsContig Editor: Group ReadingsContig Editor: Highlight DisagreementsContig Editor: Highlight DisagreementsContig Editor: highlighting readingsContig Editor: highlighting readingsContig Editor: information lineContig Editor: information lineContig Editor: joiningContig Editor: joiningContig Editor: List ConfidenceContig Editor: mode setsContig Editor: multiple editorsContig Editor: multiple editorsContig Editor: mutation reportingContig Editor: names displayContig Editor: names displayContig Editor: oligo selectionContig Editor: primer selectionContig Editor: Primer selectionContig Editor: Primer selectionContig Editor: quality valuesContig Editor: quality valuesContig Editor: quittingContig Editor: quittingContig Editor: Reference sequenceContig Editor: Reference tracesContig editor: remove readingContig Editor: Save Consensus TraceContig Editor: saving configurationContig Editor: saving configurationContig Editor: saving settingsContig Editor: saving settingsContig Editor: saving to fileContig Editor: savingContig Editor: scrollingContig Editor: searchingContig Editor: searchingContig Editor: selecting sequencesContig Editor: selectionsContig Editor: selectionsContig Editor: set active tagsContig Editor: set default confidencesContig Editor: Set or unset saving of undoContig Editor: set output listContig Editor: settings menuContig Editor: settings menuContig Editor: show consensus qualityContig Editor: show editsContig Editor: show reading qualityContig Editor: Show StrandsContig Editor: status lineContig Editor: summaryContig Editor: summaryContig Editor: tagsContig Editor: tagsContig Editor: techniquesContig Editor: template namesContig Editor: template statusContig Editor: toggle auto-saveContig Editor: Trace Display menuContig Editor: trace displayContig Editor: trace displayContig Editor: translations using feature tablesContig Editor: translationscontig joiningcontig joiningContig namescontig namingcontig namingContig navigationContig order, reset: doctor databaseContig order: Contig SelectorContig order: Contig SelectorContig regionContig Selector: changing the contig orderContig Selector: changing the contig orderContig Selector: Contig orderContig Selector: Contig orderContig Selector: menusContig Selector: menusContig Selector: saving the contig orderContig Selector: saving the contig orderContig Selector: selecting contigsContig Selector: selecting contigsContig structure: doctor databaseContig, deletion of: doctor databaseContig: template displayCONTIG_BRIEF_FORMATCONTIG_BRIEF_FORMATcontigs - identifyingcontigs - identifyingcontigs listcontigs listContigs markingContigs maskingContigs to Readings: listsContigs to Readings: listsContigs: printingContigs: saving to fileConvert program exampleConvert programconvert_trace.p4mconvert_trace: man pageconvert_traceCopy DatabaseCopy listCopy listCopy reads: dialoguecopy readsCopy sequence: spinCopy_db: man pageCopy_reads: man_pageCR: experiment file line typeCreate listCreate listcreatecreate_dialogueCreating a new databaseCross_match configurationCross_match modulecross_match_svec.p4mCrosshairs: spinCS: experiment file line typeCursor dragging:spinCursor linking:spinCursor positioning:spinCursor: contig editorCursor: contig editorCursor: spinCut sites: restriction enzymesCutoff data: contig editorCutoff data: contig editorCutoff data: TrevCutoff values: contig editorCutoff values: contig editorcutoffCutting sites: restriction enzymes:spinCV: experiment file line type
d
Dap databases: conversion to bap or gap4data hiddendatabase creationDatabase integrationdatabase limitsDatabase mergingdatabase readonly accessDatabase splittingDatabase structure: doctor databasedatabase write accessDatabase, plain text formatDatabase: backupsDatabase: busy fileDatabase: creating newDatabase: gap4 filenamesdatabase: gap4 maxdbdatabase: gap4 maxseqDatabase: lockedDatabase: maximum sizeDatabase: newDatabase: openingDatabase: readonlydatabase_namedatabase_versiondef_5_posDelete annotationsDelete contig: doctor databaseDelete ContigsDelete listDelete listDelete sequence: spindetection of mutations: introductiondiag_scoreDifference clippingdifference_clipDinucleotide frequencies:spinDiploid GraphDirected assemblyDirectories: file browserdirectories: trace filesDirectoriesDisassemble readingsDisassemble readingsDisassembly: contig editorDiscrepancies: searching for in contig editorDisplay interaction:spinDNA character setDNA translation:spinDoctor database: annotation structureDoctor database: clone structureDoctor database: contig orderDoctor database: contig structureDoctor database: database structureDoctor database: delete contigDoctor database: extending structuresDoctor database: note structureDoctor database: original clone structureDoctor database: reading structureDoctor database: reset contig orderDoctor database: shift readingsDoctor database: template structureDoctor DatabaseDot plot: spinDots: contig editor highlight disagreementsDots: contig editor highlight disagreementsDouble strandDouble stranded sequence listing:spinDR: experiment file line typeDrag and drop graphics: spinDT: experiment file line typeDump Contig: contig editorDumping results to file:spinDuplicate matches: spin
e
eba.p4meba: man pageEdit by base confidence: contig editorEdit by base type: contig editorEdit listEdit listEdit mode sets: contig editorEdit modes: contig editorEdit notebooksEditing and base accuraciesEditing techniques: confidence valuesEditing techniques: overcallsEditing techniquesEditing the sequence: TrevEditing: contig editorEditing: contig editorEditing: TrevEmail configurationEmail moduleemail.p4memail_addressemail_argsemail_progamEMBOSSEN: experiment file line typeenabledendEnter assembly configurationEnter assembly moduleenter_allenter_assembly.p4mentering annotations from fileEntering readingsEntering readingsentering tags from fileEntry boxesEntry sequence: spinerror codes in screen_seqerror codes in vector_cliperror messages: find internal joinserror messages: find internal joinserror messages: maxseqerror messages: maxseqError windowEstimate base accuracies configurationEstimate base accuracies moduleEvidence for Edit1: contig editorEvidence for Edit2: contig editorEX: experiment file line typeExample codeExample experiment fileExpected number of matches in spinExperiment File line typesExperiment file name length restrictionsExperiment file name restrictionsExperiment file name restrictionsExperiment file: exampleExperiment file: explanation of recordsExperiment file: unsupported additionsExperiment files: record typesExperiment filesExport GFFExport SequencesExport TagsExtended consensusExtending structures: doctor databaseExtension penalty for alignmentsExtract sequence configurationExtract Sequence moduleextract_fastq: man pageextract_seq.p4mextract_seq: man pageextraneous readings: filtering out
f
FakII assembly configurationFakII assembly moduleFAKII assembly: importFAKII assembly: perform and importFAKII assembly: performFAKII Assemblyfakii_assemble.p4mFASTA files: pregap4Fasta output from GapFasta output from GapFeature tables: Translation in Contig Editorfeature tablesFile browser: directoriesFile browser: filesFile browser: filtersFile browser: formatsFile browser: introductionFile browserfile formats for vectorsFile menu: Contig SelectorFile menu: Contig SelectorFile name restrictionsFile name restrictionsFile of filenames generationFile of filenames generationFile structure: SCFfile_errorfile_idfile_typeFilebrowser: TrevFiles, specifyingFiles: file browserfiltering out extraneous readingsFilters: file browserFind best diagonals: spinFind internal joins: dialogueFind internal joins: dialogueFind internal joinsFind internal joinsFind matching words: spinFind oligosFind oligosFind open reading frames:spinFind read pairs: displayFind read pairs: displayFind read pairs: exampleFind read pairs: outputFind read pairs: reading linesFind read pairs: template linesFind read pairsFind read pairsFind repeatsFind repeatsFind sequencesFind sequencesFind similar spans: spinfind_renz: man pageFinding genes: Introduction:spinfinding joinsfinding joinsfinding overlapsfinding overlapsFinding protein genes:spinFinding strings:spinFM: experiment file line typefonts, adjustingFonts, within trevFontsFontsFormat of protein score matrixformat: vector sequencesformat: vector_primer filesformat: vector_primer filesFormats: file browserformats: vector filesFunctions, builtinFunctions, in modules
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Gap penalties for alignmentsgap4 assembly limitsgap4 database limits: resettinggap4 database sizes: resettinggap4 database sizesgap4 database: maxdbgap4 database: maxseqgap4 database: reading length limitsgap4 database: resetting sizesGap4 shotgun assembly configurationGap4 shotgun assembly modulegap4: resetting assembly limitsgap4: viewing trace filesGap4gap4_assemble.p4mgaprcGene finding: Introduction:spinGeneral configuration configurationGeneral configuration modulegenerate_constraintsGenetic code:spinGenetic codeGet sequence: spinget_comment: man pageget_scf_field: man pagegetABIfield: man pageGFF: exportingGFF: importing fromGlobal variablesGoto file button, trevgraph_d_limitgraph_e_limitgraph_o_thresholdGraphics rearrangement: spinGraphics windows: user interfaceGreen, Phil (Phrap)Group Readings: contig editorGroup Readings: contig editorGTAGDB
h
Haplotype assignmentHASH= RAWDATA accessorhash_exp: man pagehash_extract: man pagehash_list: man pagehash_tar: man pageHeader record: SCFHeader: SCF structureHidden data: contig editorHidden data: contig editorhidden dataHidden datahidden datahidden datahiddenHide duplicate matches: spinHide, in Contig ComparatorHide, in Contig ComparatorHighlight Disagreements: contig editorHighlight Disagreements: contig editorHighlight readings listHighlighting readings in the editorHighlighting readings in the editorHuang: Assembly (CAP2)Huang: Assembly (CAP3)
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ID: experiment file line typeidentifying contigsidentifying contigsIgnore check databaseIgnore single templates: template displayImport GFF AnnotationsInclude config componentINFO note typeInformation line: bases in contig editorInformation line: contig editorInformation line: contig editorInformation line: contig in contig editorInformation line: contig in contig editorInformation line: readings in contig editorInformation line: readings in contig editorInformation line: tags in contig editorInformation line: tags in contig editorInformation sourcesInformation, in Contig ComparatorInformation, in Contig ComparatorInformation: Trevinit.p4minitinit_exp.p4minit_exp: man pageInitialise Experiment Files configurationInitialise Experiment files moduleInsert SizesInteraction of displays:spinInteractive clipping configurationInteractive clipping moduleinteractive_clip.p4mInterconvert t and u: spinIntroductionIntron in tRNA:spinIntron/exon boundaries:spinInvoke contig editors, in Contig ComparatorInvoke contig editors, in Contig ComparatorInvoke contig join editors, in Contig ComparatorInvoke contig join editors, in Contig ComparatorInvoke template display, in Contig ComparatorIUB codes: consensusIUB codes: consensusIUB symbols:spin
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Join EditorJoin Editorjoining contigsjoining contigs
k
keep_namesKeyboard summary (contig editor)Keyboard summary (contig editor)
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Labelling contigsLabelling readingsLE: experiment file line typeLeft mouse button: overviewleft_num_uncalledleft_win_lengthLI: experiment file line typelibraryLine thickness configurationLine types, in experiment fileList base confidenceList base confidenceList confidence: contig editorList confidenceList confidenceList LibrariesListboxLists: commandsLists: commandsLists: Contigs to ReadingsLists: Contigs to ReadingsLists: copyLists: copyLists: createLists: createLists: deleteLists: deleteLists: editLists: editLists: highlight readings listLists: loadLists: loadLists: minimal coverageLists: printLists: printLists: saveLists: saveLists: Search annotation contentsLists: search sequence namesLists: search sequence namesLists: Search template namesLists: special namesLists: special namesLists: unattached readingsListsListsLN: experiment file line typeLoad listLoad listLoad naming schemeLoad sequence: spinLocal alignment: spinlocked databaseLong readings: suggestion oflow level pregap4 configurationLT: experiment file line type
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Magic number: SCFMake_weights: man pagemakeSCF: man pagemandatoryMarking contigsmarkingmarkingMasking contigsmaskingmaskingMatch probabilities in spinmatch_fractionMatching strings:spinMatrix for alignmentsmax_extentmax_lengthmax_padsmax_pmismatchmaxdb (command line option)maxdb: gap4 assemblymaximum sequence lengthmaxseq (command line option)maxseq: find internal joinsmaxseq: find internal joinsmaxseq: gap4 assemblymaxseqMC: experiment file line typeMemory saving: spinMemory saving:spinMemory usage:spinMenus, configuringMenusMerging databasesMiddle mouse button: overviewmin_3_matchmin_5_matchmin_extentmin_lengthmin_matchminimal coverage: listsminmatchminscoreMN: experiment file line typeMode sets: contig editorModule functionsModule variablesModule, example codeMODULE_PATHModules, adding and removingModules, configuringModules, creatingModules, overviewMODULESMotif searching: percentage matches:spinMotif searching:spinmotifs: spinMouse buttons: overviewMouse control: overviewMT: experiment file line typeMultiple files in TrevMutation detection configurationMutation detection moduleMutation detection naming schemeMutation detection: introductionmutation detection: reference sequencesmutation detection: reference tracesmutation reportMutation reporting: contig editorMutation scanner modulemutation_detection.p4tMyers: Assembly (FAKII)
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N-base clippingnamenames in the editornames in the editornaming contigsnaming contigsNaming schemes, creating.naming schemes: mutation detectionnaming schemes: pregap4Naming schemesNC-IUB symbols:spinNew database creationNext button, in Contig comparatorNext button, in Contig comparatorNext button, trevno_low_complexityno_primate_rodentnocheck (command line option)Non-interactive processingNormal consensusNormal consensusNormalisation: codon usage tables:spinNote structure: doctor databaseNotes: editingNotes: selectingNotes: special typesNotesNucleotide symbolsnum_diags
o
offsetOld cloning vector clip configurationold_cloning_vector_clip.p4mOligo searchOligo searchOligo searching:spinOligo selection: contig editorOligo selection: contig editorOligos: choosing for probesON: experiment file line typeOP: experiment file line typeOpen databaseOPEN note typeOpen penalty for alignmentsOpen reading frames:spinOpening databasesOpening trace files: TrevOrdering contigs:gap4other_argsOutput annotations to fileOutput enzyme by enzyme: restriction enzymes plotOutput enzyme by enzyme: restriction enzymes plotOutput ordered on position: restriction enzymes plotOutput ordered on position: restriction enzymes plotOutput windowOvercalls: editing techniquesoverlap findingoverlap finding
p
pads: realigningPC: experiment file line typePD: primer data - the sequence of a primerPercentage matches:spinPersistence of results:spinPersonal search: spinPhrap assembly configurationPhrap assembly modulePhrap Assemblyphrap_assemble.p4mPhred configurationPhred modulephred.logphred.p4mplain textPlot stop codons: examining the plotPlot stop codons: updating the plotPlot stop codonsPlotting base composition:spinPN: experiment file line typepolyA clippingpolyA_clip: man pagepolyT clippingPR: experiment file line typepregap4.configpregap4: FASTA filespregap4: naming schemespregap4: Reference sequencepregap4: temporary filesPregap4pregap4rc filespregap4rcPrevious button, trevPrimer selection: contig editorPrimer Selection: contig editorPrimer Selection: contig editorPrimer site, definingPrimer site, findingPrimer types, ignoringPrimers: suggestion ofPrint listPrint listPrinting contigsprinting: aligned readingsPrivate data: SCFProbabilities in spinprobabilityprocess_dialogueprotein alignment symbols: spinProtein score matrix formatProtein:spinPS: experiment file line type
q
Qclip: man pageQL: experiment file line typeQR: experiment file line typeQuality calculation algorithmQuality calculation algorithmquality clip configurationQuality clip endsQuality clip moduleQuality clippingQuality codesQuality in contig editorQuality plot: examining the plotQuality plot: template displayQuality plotQuality values - use ofQuality values: contig editor, displayedQuality values: contig editor, use withinQuality values: contig editor, use withinQuality: output for consensusquality_clip.p4mquality_clipQuit: TrevQuitting: contig editorQuitting: contig editor
r
Range: spinRAWD note typeRAWDATARead groups: SAM RG tagsRead pair data and contig orderingRead pairsRead pairsread raidRead sequence: spinRead-pair coverageRead-pairs, trace displayREAD_BRIEF_FORMATREAD_BRIEF_FORMATread_only (command line option)reading clippingReading coverageReading frame:spinreading length limits in gap4Reading name length restrictionsReading name restrictionsReading name restrictionsreading names in the editorreading names in the editorReading names, searching forReading names, searching forReading namesReading numbersreading percent mismatchreading percent mismatchReading plot: template displayReading structure: doctor databaseReadings list: template displayreadings listreadings listreadings: copying to other databasesreadings: enteringreadings: extraneousReadings: maximum in a databasereadings: sorted on alignment scorereadings: sorted on alignment scorereadonly databasereadonlyreads: copying to other databasesrealigning sequencesRecords in experiment filesRedirect outputReference sequence: contig editorReference sequence: pregap4reference sequencesReference trace moduleReference traces: contig editorreference tracesreferencesReject button, trevRemove Contig HolesRemove Pad ColumnsRemove reading: contig editorRemove, in Contig ComparatorRemove, in Contig ComparatorRemoving contigsremoving extraneous readingsRemoving modulesRemoving readingsRemoving readingsRemoving resultsRemoving resultsRepeat searchRepeat searchrepeat_filerepeat_masker.p4mRepeatMasker configurationRepeatMasker modulerepeats_masker.p4mReport mutations: contig editorreportRestriction enzyme filesRestriction enzyme sites:spinRestriction enzymes: configuring: spinRestriction enzymes: configuringRestriction enzymes: configuringRestriction enzymes: cut sitesRestriction enzymes: examining the plot: spinRestriction enzymes: examining the plotRestriction enzymes: examining the plotRestriction enzymes: introduction: spinRestriction enzymes: selecting enzymes: spinRestriction enzymes: selecting enzymesRestriction enzymes: selecting enzymesRestriction enzymes: tags, creation ofRestriction enzymes: template displayRestriction enzymes: textual outputRestriction enzymes: textual outputRestriction enzymesRestriction enzymesRestriction site listing:spinRestriction site printing:spinRestrictions on experiment file namesRestrictions on file namesRestrictions on reading namesRestrictions on sample namesRestrictions on SCF file namesResults manager: introductionResults manager: introductionResults manager: spinResults managerResults managerResults menu: Contig SelectorResults menu: Contig SelectorResults: removingResults: removingRight mouse button: overviewright_num_uncalledright_win_lengthRotate sequence: spinRS: experiment file line typeRuler: template displayRun commandrun
s
sample name restrictionsSample name restrictionsSample points: SCFSamples1: SCF structureSamples2: SCF structureSanger Centre naming scheme, newSanger Centre naming scheme, oldsanger_names_new.p4tsanger_names_old.p4tSave AsSave Consensus Trace: contig editorSave listSave listSave sequence: spinsaving contigs to fileSaving: contig editorSaving: TrevSC: experiment file line typeSCScaling: TrevSCF file name restrictionsSCF file name restrictionsSCF header recordSCF magic numberSCF: byte orderingSCF: commentsSCF: file structureSCF: private dataSCF: Sample pointsSCF: sequenceSCFScore matrix formatscoreScramble sequence: spinScreen for unclipped vector configurationScreen for unclipped vector moduleScreen only: assemblyScreen sequences configurationScreen sequences modulescreen_filescreen_modescreen_seq, limitsscreen_seq.p4mScreen_seq: error codesScreen_seq: error codesscreen_seq: man pageScreen_seqscreen_seqscreen_vector.p4mScreening against vector sequencescreening for bacterial sequencesscreening for vectorsScreening readings for contaminant sequencesScroll on outputSE: experiment file line typeSearch annotation contents: listsSearch from fileSearch sequence names: listsSearch sequence names: listsSearch template names: listsSearch: in the output windowSearching by annotation comments: contig editorSearching by consensus discrepancies: contig editorSearching by consensus quality: contig editorSearching by discrepancies: contig editorSearching by edits: contig editorSearching by Evidence for Edit1: contig editorSearching by Evidence for Edit2: contig editorSearching by file: contig editorSearching by position: contig editorSearching by problem: contig editorSearching by quality: contig editorSearching by sequence: contig editorSearching by tag type: contig editorSearching by Verify AND: contig editorSearching for motifs:spinSearching for oligos:spinSearching for strings:spinSearching reading name: contig editorSearching: contig editorSearching: contig editorSearching: motifs:spinSearching: open reading frames:spinSearching: protein genes:spinSearching: splice sites:spinSearching: start codons:spinSearching: stop codons:spinSearching: TrevSearching: tRNA genes:spinSearching:spinSecond highest confidence graphsecuritySelect tags: template displaySelecting a sequence: spinselecting contigs: Contig Selectorselecting contigs: Contig SelectorSelecting sequences: contig editorSelections: contig editorSelections: contig editorSeq identifier: spinSequence composition:spinSequence display: spinSequence display:spinSequence interpretation: finding protein genes:spinSequence interpretation: tRNA gene search:spinsequence length, maximumSequence manager: spinSequence names, searching forSequence names, searching forSequence scrolling:spinSequence SearchSequence SearchSequence viewer:spinSequence: SCFsequence_vector_clip.p4mSequencing vector clip configurationSequencing vector clip moduleSet Active Tags: contig editorSet Default Confidences: contig editorSet genetic code:spinSet genetic codeSet or unset saving of undo: contig editorSet Output List: contig editorSet the range: spinSettings menu: contig editorSettings menu: contig editorSettings: saving in contig editorSettings: saving in contig editorSF: experiment file line typeSFSFF= RAWDATA accessorShift readings: doctor databaseShotgun assemblyShow consensus quality: contig editorShow Edits: contig editorShow only read pairs: template displayShow read-pair TracesShow reading quality: contig editorShow relationshipsShow Strands: contig editorShow template namesShow unpadded positionsshuffle padsShuffle PadsShutdown configurationshutdown.p4mshutdownSI: experiment file line typeSignificance of matches in spinSim: spinSimple search: spinSimple Text Databasesimple_onlysimultaneous database accessSingle stranded regions: assembling intoSingle stranded sequence listing:spinSites: restriction enzymes:spinSL: experiment file line typeSmith-Waterman: spinSNP candidatesSort MatchesSort MatchesSP: experiment file line typeSPSPIN Sequence Comparison Plot: spinSPIN Sequence Plot: spinSpin: copy sequenceSpin: sequence type (linear or circular)SpinSplice junctions:spinSplice sites:spinSplitting databasesSQ: experiment file line typeSR: experiment file line typeSS: experiment file line typeST: experiment file line typeStart codons:spinstartStatus line: contig editorStatus line: contig editorStems and loops:spinStop codons displayStop codons: examining the plotStop codons: updating the plotStop codons:spinStops: suggested experimentsstrand coverageString finding:spinString matching:spinstring searchstring searchString searching:spinStyles of windowsSubsequence searching:spinSuggest long readingsSuggest primersSuggest probesSummary of editing commands: contig editorSummary of editing commands: contig editorSummary: contig editorSummary: contig editorSuper contigsSuperedit: contig editorSV: experiment file line type
t
Tag databaseTag repeats configurationTag repeats moduleTag SelectorTAG_BRIEF_FORMATTAG_BRIEF_FORMATtag_repeats.p4mtag_typetag_typesTags, searching forTags: contig editorTags: contig editortags: entering from a fileTags: restriction enzymes plotTags: template displayTagsTAR= RAWDATA accessorTC: experiment file line typeTechniques of editingTemplate display and contig orderingTemplate display: active readingsTemplate display: contigTemplate display: ignore single templatesTemplate display: quality plotTemplate Display: reading plotTemplate display: readings listTemplate display: restriction enzymesTemplate display: rulerTemplate display: select tagsTemplate display: show only read pairsTemplate display: tagsTemplate Display: template plotTemplate DisplayTemplate DisplayTemplate names, searching forTemplate plot: template displayTemplate size toleranceTemplate Status CodesTemplate StatusTemplate structure: doctor databaseTemplate: find read pairsTemplates: grouping readings in contig editortemporary filesText windowsTG: experiment file line typetg_indexTips on assemblytk_utilsrcTN: experiment file line typeto_scf.p4mToggle auto-save: contig editorTrace difference moduleTrace differences: contig editorTrace differences: Y scalingTrace Display menu: contig editorTrace displays: contig editorTrace displays: contig editorTrace file locationtrace files: defining locationtrace files: locationTrace Format Conversion configurationTrace Format ConversionTrace: Consensus Tracetrace_diff.p4mtrace_dump: man pagetracediff: man pageTranscribe sequence: spinTranslate sequence: spinTranslation to protein:spinTranslations: contig editorTrev: editing the sequenceTrev: editingTrev: fontsTrev: informationTrev: introductionTrev: opening trace filesTrev: page optionsTrev: paper optionsTrev: print fontsTrev: print panelsTrev: printing a traceTrev: quitTrev: saving a trace fileTrev: scalingTrev: searchingTrev: setting cutoffsTrev: trace print basesTrev: trace print colour and line widthTrev: trace print dash patternTrev: trace print exampleTrev: trace print magnificationTrev: trace print optionsTrev: trace print titleTrev: undoTrev: vector sequenceTrevtRNA gene search:spintRNA introns:spin
u
Unattached readings: listsUncalled base clip configurationuncalled_clip.p4mUndo clip edits, trevUndo toggle: contig editorUndo: contig editorUneven positional base frequencies:spinUnfinished consensusUnpadded base positionsUnpadded base positionsUnpadded positions in editorUpdate contig orderupdate_exp_fileupdate_expfileURL= RAWDATA accessoruse_sample_nameuse_vp_fileUser interface: buttonsUser interface: colour selectorUser interface: entry boxesUser interface: introductionUser interface: menusUser interface: text windowsUser interface: Zooming graphicsUser interfaceUser levels
v
Variables, global to all modulesVariables, in modulesvector file formatsVector sequence: screeningvector sequences formatVector_Clip: cloning site, definingVector_Clip: error codesVector_Clip: error codesvector_clip: man pageVector_Clip: primer site, definingVector_Clipvector_filevector_listVector_primer filesVector_Primer filesVectors, in TrevVerfiy AND: contig editorVerfiy OR: contig editorView menu: Contig SelectorView menu: Contig Selectorvp_filevp_length
w
Weight matrix: splice sites:spinWeight matrix:spinWindow styleswindow_lengthword_lengthWT: wild type trace fileWT
y
Y scale differences
z
Zoom: spinZooming graphicsZTR Chunk formatZTR Chunk typesZTR headerZTR ReferencesZTR Text IdentifiersZTR
This document was generated using the merge_indexes.pl program.
Last generated on 25 November 2011.