CSC

	Tehdyt toimenpiteet Index - . 3 A B C D E F G H I J K L M N O P Q R S T U V - -check -maxdb -maxseq -no_exec_notes -no_rawdata_note -nocheck -read_only . .gaprc .tk_utilsrc 3 3 Character Amino Acids: contig editor a Active tags Align: contig editor aligned readings: printing aligned readings: saving to file aligned readings: sorted on alignment score aligning pads: contig editor Alignment matrix file Alignment scores allcontigs list Allow del any in cons: contig editor Allow del dash cons: contig editor Allow del in read: contig editor Allow insert any in cons: contig editor Allow insert in read: contig editor Allow reading shift: contig editor Allow replace in cons: contig editor Allow transpose any: contig editor Allow uppercase: contig editor allreadings list Annotating contigs Annotating readings Annotation Selector Annotation structure: doctor database Annotations, searching for Annotations: contig editor Annotations: deleting (Doctor Database) annotations: entering from a file Annotations: outputting to file (Doctor Database) Assemble: independently i.e. ignoring previous data Assembly assembly problems: breaking contigs assembly problems: disassembling readings assembly problems: removing readings Assembly: CAP2 Assembly: CAP3 Assembly: CAP3 information Assembly: directed Assembly: failure codes Assembly: FAKII Assembly: Huang Assembly: import CAP2 Assembly: import CAP3 Assembly: import FAKII Assembly: into new contigs Assembly: into one contig Assembly: into separate contigs Assembly: large projects Assembly: limits Assembly: maxdb Assembly: maxseq Assembly: Myers Assembly: perform and import CAP2 Assembly: perform and import CAP3 Assembly: perform and import FAKII Assembly: perform CAP2 Assembly: perform CAP3 Assembly: perform FAKII Assembly: Phrap Assembly: resetting limits Assembly: screen only Assembly: shotgun Assembly: single stranded regions Assembly: stack readings Assembly: stand alone CAP2 Assembly: stand alone CAP3 Assembly: tips Auto-display Traces: contig editor Auto-save: contig editor b Backing up databases Bap databases: conversion to gap4 Base accuracies - use of BASE_BRIEF_FORMAT1 BASE_BRIEF_FORMAT2 Break contig Break contig: contig editor Busy file BUSY files c Calculate consensus Calculate consensus: algorithm Calculate consensus: confidence Calculate consensus: extended consensus Calculate consensus: normal consensus Calculate consensus: quality Calculate consensus: reliability Calculate consensus: unfinished consensus CAP2 Assembly CAP2 assembly: import CAP2 assembly: perform CAP2 assembly: perform and import CAP2 assembly: stand alone CAP3 Assembly CAP3 assembly: import CAP3 assembly: information CAP3 assembly: perform CAP3 assembly: perform and import CAP3 assembly: stand alone check (command line option) Check assembly Check database Check database: annotation checks Check database: clone checks Check database: contig checks Check database: database checks Check database: ignoring Check database: note checks Check database: reading checks Check database: template checks Check database: vector checks Clipping by differences Clipping by quality Clipping within Gap4 Clone structure: doctor database CLOS note type Colour blindness Colour configuration window Colour: contig editor highlight disagreements Command line arguments Commands menu: contig editor Comparator window Compare Strands: contig editor Complement contig Compressions: suggested experiments Confidence in contig editor Confidence of consensus Confidence values - use of Confidence values graph Confidence values: editing techniques Configure menus configure: contig editor Configure: restriction enzymes Consensus algorith in contig editor Consensus calculation confidence Consensus calculation method consensus IUB codes Consensus Trace Consensus: contig editor Consensus: outputting Consistency display Contig breaking Contig Comparator Contig comparator: auto navigation Contig Comparator: manipulating results Contig comparator: next button Contig complementing Contig Editor: 3 Character Amino Acids Contig Editor: align Contig Editor: allow del any in cons Contig Editor: allow del dash in cons Contig Editor: Allow del in read Contig Editor: allow insert any in cons Contig Editor: allow insert in read Contig Editor: allow reading shift Contig Editor: allow replace in cons Contig Editor: allow transpose any Contig Editor: allow uppercase Contig Editor: annotations Contig Editor: auto-display traces Contig Editor: auto-save Contig editor: break contig Contig Editor: commands menu Contig Editor: Compare Strands Contig editor: confidence values Contig Editor: cursor Contig Editor: cursor movement Contig Editor: cutoff data Contig Editor: cutoff values Contig editor: disassemble readings Contig Editor: Dump Contig Contig Editor: edit by base confidence Contig Editor: edit by base type Contig Editor: edit mode sets Contig Editor: edit modes Contig Editor: editing features Contig Editor: editing keys Contig Editor: editing techniques Contig Editor: group readings by templates Contig Editor: Highlight Disagreements Contig Editor: highlighting readings Contig Editor: information line Contig Editor: joining Contig Editor: List Confidence Contig Editor: mode sets Contig Editor: multiple editors Contig Editor: mutation reporting Contig Editor: names display Contig Editor: oligo selection Contig Editor: primer selection Contig Editor: Primer selection Contig Editor: quality values Contig Editor: quitting Contig Editor: Reference sequence Contig Editor: Reference traces Contig editor: remove reading Contig Editor: Save Consensus Trace Contig Editor: saving Contig Editor: saving configuration Contig Editor: saving settings Contig Editor: saving to file Contig Editor: searching Contig Editor: selections Contig Editor: set active tags Contig Editor: set default confidences Contig Editor: Set or unset saving of undo Contig Editor: set output list Contig Editor: settings menu Contig Editor: show consensus quality Contig Editor: show edits Contig Editor: show reading quality Contig Editor: Show Strands Contig Editor: shuffle Pads Contig Editor: status line Contig Editor: summary Contig Editor: tags Contig Editor: techniques Contig Editor: toggle auto-save Contig Editor: Trace differences Contig Editor: trace display Contig Editor: Trace Display menu Contig Editor: translations Contig Editor: translations using feature tables contig joining Contig names contig naming Contig order, reset: doctor database Contig order: Contig Selector Contig Selector: changing the contig order Contig Selector: Contig order Contig Selector: menus Contig Selector: saving the contig order Contig Selector: selecting contigs Contig structure: doctor database Contig, deletion of: doctor database Contig: template display CONTIG_BRIEF_FORMAT contigs - identifying contigs list Contigs marking Contigs masking Contigs to Readings: lists Contigs: printing Contigs: saving to file Convert program Convert program example Copy Database Copy list copy reads Copy reads: dialogue Create list Creating a new database Cursor: contig editor Cut sites: restriction enzymes Cutoff data: contig editor Cutoff values: contig editor d Dap databases: conversion to bap or gap4 data hidden database limits Database merging database readonly access Database splitting Database structure: doctor database database write access Database: backups Database: busy file Database: creating new Database: gap4 filenames database: gap4 maxdb database: gap4 maxseq Database: locked Database: maximum size Database: new Database: opening Database: readonly Delete annotations Delete contig: doctor database Delete list Difference clipping Directed assembly Directories directories: trace files Disassemble readings Disassembly: contig editor Discrepancies: searching for in contig editor Doctor Database Doctor database: annotation structure Doctor database: clone structure Doctor database: contig order Doctor database: contig structure Doctor database: database structure Doctor database: delete contig Doctor database: extending structures Doctor database: note structure Doctor database: original clone structure Doctor database: reading structure Doctor database: reset contig order Doctor database: shift readings Doctor database: template structure Dots: contig editor highlight disagreements Double strand Dump Contig: contig editor e Edit by base confidence: contig editor Edit by base type: contig editor Edit list Edit mode sets: contig editor Edit modes: contig editor Edit notebooks Editing and base accuracies Editing techniques Editing techniques: confidence values Editing techniques: overcalls Editing: contig editor entering annotations from file Entering readings entering tags from file error messages: find internal joins error messages: maxseq Evidence for Edit1: contig editor Evidence for Edit2: contig editor Experiment file name length restrictions Experiment file name restrictions Extended consensus Extending structures: doctor database Extension penalty for alignments f FAKII Assembly FAKII assembly: import FAKII assembly: perform FAKII assembly: perform and import Fasta output from Gap Feature tables: Translation in Contig Editor File menu: Contig Selector File name restrictions File of filenames generation Find internal joins Find internal joins: dialogue Find oligos Find read pairs Find read pairs: display Find read pairs: example Find read pairs: output Find read pairs: reading lines Find read pairs: template lines Find repeats Find sequences finding joins finding overlaps fonts, adjusting g Gap penalties for alignments Gap4 gap4 assembly limits gap4 database limits: resetting gap4 database sizes gap4 database sizes: resetting gap4 database: maxdb gap4 database: maxseq gap4 database: reading length limits gap4 database: resetting sizes gap4: resetting assembly limits gap4: viewing trace files gaprc Genetic code Green, Phil (Phrap) Group Readings by Templates: contig editor GTAGDB h Hidden data hidden data Hidden data: contig editor Hide, in Contig Comparator Highlight Disagreements: contig editor Highlighting readings in the editor Huang: Assembly (CAP2) Huang: Assembly (CAP3) i identifying contigs Ignore check database Ignore single templates: template display INFO note type Information line: bases in contig editor Information line: contig editor Information line: contig in contig editor Information line: readings in contig editor Information line: tags in contig editor Information, in Contig Comparator Invoke contig editors, in Contig Comparator Invoke contig join editors, in Contig Comparator Invoke template display, in Contig Comparator IUB codes: consensus j Join Editor joining contigs k Keyboard summary (contig editor) l Labelling contigs Labelling readings Line thickness configuration List confidence List confidence: contig editor Listbox Lists Lists: commands Lists: Contigs to Readings Lists: copy Lists: create Lists: delete Lists: edit Lists: load Lists: minimal coverage Lists: print Lists: save Lists: Search annotation contents Lists: search sequence names Lists: Search template names Lists: special names Lists: unattached readings Load list locked database Long readings: suggestion of m marking Marking contigs masking Masking contigs Matrix for alignments maxdb (command line option) maxdb: gap4 assembly maximum sequence length maxseq maxseq (command line option) maxseq: find internal joins maxseq: gap4 assembly Menus, configuring Merging databases minimal coverage: lists Mode sets: contig editor Mutation detection: Group Readings by Templates Mutation reporting: contig editor Myers: Assembly (FAKII) n names in the editor naming contigs New database creation Next button, in Contig comparator nocheck (command line option) Normal consensus Note structure: doctor database Notes Notes: editing Notes: selecting Notes: special types o Oligo search Oligo selection: contig editor Oligos: choosing for probes OPEN note type Open penalty for alignments Opening databases Ordering contigs:gap4 Output annotations to file Output enzyme by enzyme: restriction enzymes plot Output ordered on position: restriction enzymes plot Overcalls: editing techniques overlap finding p pad alignment: contig editor pad shuffling: contig editor Phrap Assembly Plot stop codons Plot stop codons: examining the plot Plot stop codons: updating the plot Primer Selection: contig editor Primer selection: contig editor Primers: suggestion of Print list Printing contigs printing: aligned readings q Quality calculation algorithm Quality clipping Quality codes Quality in contig editor Quality plot Quality plot: examining the plot Quality plot: template display Quality values - use of Quality values: contig editor, displayed Quality values: contig editor, use within Quality: output for consensus Quitting: contig editor r RAWD note type RAWDATA Read pair data and contig ordering Read pairs read raid Read-pair coverage READ_BRIEF_FORMAT read_only (command line option) Reading coverage reading length limits in gap4 Reading name length restrictions Reading name restrictions Reading names reading names in the editor Reading names, searching for Reading numbers reading percent mismatch Reading plot: template display Reading structure: doctor database readings list Readings list: template display readings: copying to other databases readings: entering Readings: maximum in a database readings: sorted on alignment score readonly readonly database reads: copying to other databases Reference sequence: contig editor Reference traces: contig editor Remove reading: contig editor Remove, in Contig Comparator Removing readings Removing results Repeat search Report mutations: contig editor Restriction enzymes Restriction enzymes: configuring Restriction enzymes: cut sites Restriction enzymes: examining the plot Restriction enzymes: selecting enzymes Restriction enzymes: tags, creation of Restriction enzymes: template display Restriction enzymes: textual output Results manager Results manager: introduction Results menu: Contig Selector Results: removing Ruler: template display s sample name restrictions Save As Save Consensus Trace: contig editor Save list saving contigs to file Saving: contig editor SCF file name restrictions Screen only: assembly Search annotation contents: lists Search sequence names: lists Search template names: lists Searching by annotation comments: contig editor Searching by consensus quality: contig editor Searching by discrepancies: contig editor Searching by edits: contig editor Searching by Evidence for Edit1: contig editor Searching by Evidence for Edit2: contig editor Searching by file: contig editor Searching by position: contig editor Searching by problem: contig editor Searching by quality: contig editor Searching by sequence: contig editor Searching by tag type: contig editor Searching by Verify AND: contig editor Searching reading name: contig editor Searching: contig editor security Select tags: template display selecting contigs: Contig Selector Selections: contig editor sequence length, maximum Sequence names, searching for Sequence Search Set Active Tags: contig editor Set Default Confidences: contig editor Set genetic code Set or unset saving of undo: contig editor Set Output List: contig editor Settings menu: contig editor Settings: saving in contig editor Shift readings: doctor database Shotgun assembly Show consensus quality: contig editor Show Edits: contig editor Show only read pairs: template display Show reading quality: contig editor Show relationships Show Strands: contig editor Show unpadded positions Shuffle Pads: contig editor simultaneous database access Single stranded regions: assembling into Sort Matches Splitting databases Status line: contig editor Stop codons display Stop codons: examining the plot Stop codons: updating the plot Stops: suggested experiments strand coverage string search Suggest long readings Suggest primers Suggest probes Summary of editing commands: contig editor Summary: contig editor Super contigs Superedit: contig editor t Tag database Tag Selector TAG_BRIEF_FORMAT Tags Tags, searching for Tags: contig editor tags: entering from a file Tags: restriction enzymes plot Tags: template display Techniques of editing Template Display Template display and contig ordering Template display: active readings Template display: contig Template display: ignore single templates Template display: quality plot Template Display: reading plot Template display: readings list Template display: restriction enzymes Template display: ruler Template display: select tags Template display: show only read pairs Template display: tags Template Display: template plot Template names, searching for Template plot: template display Template structure: doctor database Template: find read pairs Templates: grouping readings in contig editor Tips on assembly tk_utilsrc Toggle auto-save: contig editor Trace differences: contig editor Trace Display menu: contig editor Trace displays: contig editor Trace file location trace files: defining location trace files: location Trace: Consensus Trace Translations: contig editor u Unattached readings: lists Undo toggle: contig editor Undo: contig editor Unfinished consensus Unpadded base positions Unpadded positions in editor Update contig order User levels v Verfiy AND: contig editor Verfiy OR: contig editor View menu: Contig Selector This page is maintained by staden-package. Last generated on 25 April 2003. URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_177.html