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Index

- . 3 A B C D E F G H I J L M N O P Q R S T U V

-

  • -check
  • -maxdb
  • -maxseq
  • -no_exec_notes
  • -no_rawdata_note
  • -nocheck
  • -read_only
  • .

  • .gaprc file
  • 3

  • 3 Character Amino Acids: contig editor
  • a

  • Active tags
  • Align: contig editor
  • aligning pads: contig editor
  • 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: contig editor
  • Annotations: deleting (Doctor Database)
  • Annotations: outputting to file (Doctor Database)
  • Assemble: independently i.e. ignoring previous data
  • Assembly
  • 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: 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: preassembled data
  • Assembly: screen only
  • Assembly: shotgun
  • Assembly: single stranded regions
  • 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 gap
  • Base accuracies - use of
  • BASE_BRIEF_FORMAT1
  • BASE_BRIEF_FORMAT2
  • Break contig
  • Break contig: contig editor
  • Busy file
  • 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: introduction
  • 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: editing techniques
  • Configure Cutoffs
  • Configure: restriction enzymes
  • Consensus calculation confidence
  • Consensus calculation method
  • Consensus: outputting
  • 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: Diff against consensus trace
  • Contig Editor: Diff against specific trace
  • 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: introduction
  • Contig Editor: joining
  • Contig Editor: List Confidence
  • Contig Editor: mode sets
  • Contig Editor: multiple editors
  • Contig Editor: names display
  • Contig Editor: normal mode (trace display)
  • Contig Editor: oligo selection
  • Contig Editor: Primer selection
  • Contig Editor: primer selection
  • Contig Editor: quality values
  • Contig Editor: quitting
  • Contig editor: remove reading
  • Contig Editor: Save Consensus Trace
  • Contig Editor: saving
  • Contig Editor: searching
  • Contig Editor: selections
  • Contig Editor: set active tags
  • Contig Editor: set default confidences
  • 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 display
  • Contig Editor: Trace Display menu
  • Contig Editor: translations
  • 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: introduction
  • 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
  • Convert program
  • Convert program example
  • Copy Database
  • Copy list
  • 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 gap
  • data hidden
  • Database merging
  • Database splitting
  • Database structure: doctor database
  • Database: backups
  • Database: busy file
  • Database: creating new
  • Database: gap filenames
  • Database: new
  • Database: opening
  • Delete annotations
  • Delete contig: doctor database
  • Delete list
  • Diff against consensus trace: contig editor
  • Diff against specific trace: contig editor
  • Difference clipping
  • Directed assembly
  • Directories
  • 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: introduction
  • 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
  • Enter pre-assembled data
  • Entering readings
  • 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
  • f

  • FAKII Assembly
  • FAKII assembly: import
  • FAKII assembly: perform
  • FAKII assembly: perform and import
  • Fasta output from Gap
  • file location: trace file location
  • 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
  • finding joins
  • finding overlaps
  • Fonts
  • g

  • gap4: mutation detection
  • 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
  • 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
  • j

  • Join Editor
  • joining contigs
  • 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: introduction
  • Lists: load
  • Lists: minimal coverage
  • Lists: print
  • Lists: save
  • Lists: special names
  • Lists: unattached readings
  • Load list
  • Long readings: suggestion of
  • m

  • marking
  • Marking contigs
  • masking
  • Masking contigs
  • maxdb (command line option)
  • Maxseq
  • maxseq (command line option)
  • maxseq: find internal joins
  • Merging databases
  • minimal coverage: lists
  • Mode sets: contig editor
  • mutation checking in gap4
  • Myers: Assembly (FAKII)
  • n

  • names in the editor
  • naming contigs
  • netscape
  • New database creation
  • Next button, in Contig comparator
  • nocheck (command line option)
  • Normal consensus
  • normal mode (trace display): contig editor
  • Note structure: doctor database
  • Notes
  • Notes: editing
  • Notes: introduction
  • Notes: selecting
  • Notes: special types
  • o

  • Oligo search
  • Oligo selection: contig editor
  • Oligos: choosing for probes
  • OPEN note type
  • Opening databases
  • Options menu
  • 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
  • path for trace files: RAWDATA
  • Phrap Assembly
  • Plot stop codons
  • Plot stop codons: examining the plot
  • Plot stop codons: updating the plot
  • Preassembled data: assembly
  • Primer Selection: contig editor
  • Primer selection: contig editor
  • Primers: suggestion of
  • Print list
  • q

  • Quality calculation
  • Quality clipping
  • Quality codes
  • Quality in contig editor
  • Quality plot: examining the plot
  • Quality plot: introduction
  • 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: trace file location
  • Read pair data and contig ordering
  • Read pairs
  • READ_BRIEF_FORMAT
  • read_only (command line option)
  • Reading name length restrictions
  • Reading name restrictions
  • Reading names
  • reading names in the editor
  • Reading numbers
  • Reading plot: template display
  • Reading structure: doctor database
  • readings list
  • Readings list: template display
  • readings: entering
  • Remove reading: contig editor
  • Remove, in Contig Comparator
  • Removing readings
  • Removing results
  • Repeat search
  • Restriction enzymes: configuring
  • Restriction enzymes: cut sites
  • Restriction enzymes: examining the plot
  • Restriction enzymes: introduction
  • 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: contig editor
  • SCF file name restrictions
  • Screen only: assembly
  • 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 by Verify OR: contig editor
  • Searching reading name: contig editor
  • Searching: contig editor
  • Select tags: template display
  • selecting contigs: Contig Selector
  • Selections: contig editor
  • Set Active Tags: contig editor
  • Set Default Confidences: contig editor
  • Set Fonts
  • Set maxseq
  • Set Output List: contig editor
  • Settings menu: 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
  • Shuffle Pads: contig editor
  • 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
  • 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: contig editor
  • 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: introduction
  • 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 plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Templates: grouping readings in contig editor
  • Tips on assembly
  • Toggle auto-save: contig editor
  • Trace Display menu: contig editor
  • Trace displays: contig editor
  • Trace displays: RAWDATA
  • Trace displays: trace file location
  • trace_diff: checking results in gap4
  • Translations: contig editor
  • u

  • Unattached readings: lists
  • Unfinished consensus
  • Unpadded base positions
  • Update contig order
  • v

  • Verfiy AND: contig editor
  • Verfiy OR: contig editor
  • View menu: Contig Selector

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    This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_157.html