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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

-

  • -maxdb
  • -maxseq
  • -read_only

    • .

  • .gaprc file

    • 3

  • 3 Character Amino Acids: contig editor

    • a

  • Active tags
  • Align: contig editor
  • Annotating contigs
  • Annotating readings
  • 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: directed
  • Assembly: failure codes
  • Assembly: into new contigs
  • Assembly: into one contig
  • Assembly: preassembled data
  • Assembly: screen only
  • Assembly: shotgun
  • Assembly: single stranded regions
  • Assembly: tips
  • Auto-display Traces: contig editor
  • Auto-save: contig editor

    • b

  • Backing up databases
  • Bap databases: conversion to gap
  • Base accuracies - use of
  • Break contig
  • Busy file

    • c

  • Calculate consensus
  • Calculate consensus: algorithm
  • Calculate consensus: extended consensus
  • Calculate consensus: normal consensus
  • Calculate consensus: quality
  • Calculate consensus: unfinished consensus
  • Check assembly
  • Check database
  • Check database: annotation checks
  • Check database: clone checks
  • Check database: contig checks
  • Check database: database checks
  • Check database: introduction
  • Check database: reading checks
  • Check database: template checks
  • Check database: vector checks
  • Clone structure: doctor database
  • Colour blindness
  • Colour configuration window
  • Command line arguments
  • Commands menu: contig editor
  • Compare Strands: contig editor
  • Compressions: suggested experiments
  • Configure Cutoffs
  • Configure: restriction enzymes
  • Consensus calculation method
  • Consensus: outputting
  • Contig Editor: 3 Character Amino Acids
  • Contig Editor: align
  • Contig Editor: annotations
  • Contig Editor: auto-display traces
  • Contig Editor: auto-save
  • Contig Editor: commands menu
  • Contig Editor: Compare Strands
  • Contig Editor: cursor movement
  • Contig Editor: cutoff data
  • Contig Editor: cutoff values
  • Contig Editor: Dump Contig
  • Contig Editor: editing features
  • Contig Editor: editing keys
  • Contig Editor: editing modes
  • Contig Editor: Highlight Disagreements
  • Contig Editor: highlighting readings
  • Contig Editor: inserting bases
  • Contig Editor: introduction
  • Contig Editor: joining
  • Contig Editor: multiple editors
  • Contig Editor: names display
  • Contig Editor: pads
  • Contig Editor: Primer selection
  • Contig Editor: quality values
  • Contig Editor: quitting
  • Contig Editor: saving
  • Contig Editor: searching
  • Contig Editor: selections
  • Contig Editor: set active tags
  • Contig Editor: set output list
  • Contig Editor: settings menu
  • Contig Editor: shifting readings
  • Contig Editor: show quality
  • Contig Editor: Show Strands
  • Contig Editor: Shuffle Pads
  • Contig Editor: status line
  • Contig Editor: summary
  • Contig Editor: tags
  • Contig Editor: toggle auto-save
  • Contig Editor: trace display
  • Contig Editor: translations
  • 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: saving the contig order
  • Contig Selector: selecting contigs
  • Contig Selector: view menu
  • Contig structure: doctor database
  • Contig, deletion of: doctor database
  • contigs - identifying
  • Contigs marking
  • Contigs masking
  • Convert program
  • Convert program example
  • Copy list
  • Create list
  • Creating a new database
  • Cut sites: restriction enzymes
  • Cutoff data: contig editor
  • Cutoff values: contig editor

    • d

  • Dap databases: conversion to bap or gap
  • data hidden
  • 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
  • Directed assembly
  • Disassemble readings
  • 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: original clone structure
  • Doctor database: reading structure
  • Doctor database: reset contig order
  • Doctor database: shift readings
  • Doctor database: template structure
  • Doctor database: vector structure
  • Double strand
  • Dump Contig: contig editor

    • e

  • Edit list
  • Editing and base accuracies
  • Editing modes: contig editor
  • Editing: contig editor
  • Enter pre-assembled data
  • Entering readings
  • Extended consensus
  • Extending structures: doctor database

    • f

  • Fasta output from Gap
  • 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

    • g

  • GTAGDB

    • h

  • Hidden data
  • Hidden data: contig editor
  • Highlight Disagreements: contig editor
  • Highlighting readings in the editor

    • i

  • identifying contigs
  • Ignore single templates: template display
  • Insertion and deletion of bases: contig editor

    • j

  • Join Editor

    • l

  • Labelling contigs
  • Labelling readings
  • Line thickness configuration
  • Lists
  • Lists: commands
  • Lists: copy
  • Lists: create
  • Lists: delete
  • Lists: edit
  • Lists: introduction
  • Lists: load
  • Lists: minimal coverage
  • Lists: save
  • Lists: unattached readings
  • Load list
  • Long readings: suggestion of

    • m

  • Marking contigs
  • Masking contigs
  • maxdb
  • maxseq
  • minimal coverage: lists

    • n

  • naming contigs
  • netscape
  • New database creation
  • Normal consensus

    • o

  • Oligo search
  • Oligo selection: contig editor
  • Oligos: choosing for probes
  • Opening databases
  • Options menu
  • Output annotations to file

    • p

  • Pads: contig editor
  • Plot stop codons
  • Plot stop codons: examining the plot
  • Plot stop codons: updating the plot
  • Preassembled data: assembly
  • Primer Selection: contig editor
  • Primers: suggestion of

    • q

  • Quality calculation
  • Quality codes
  • Quality plot: template display
  • Quality values: contig editor, displayed
  • Quality values: contig editor, use within
  • Quality: output for consensus
  • Quitting: contig editor

    • r

  • Read pairs
  • read_only
  • Reading names
  • Reading numbers
  • Reading plot: template display
  • Reading structure: doctor database
  • Readings list: template display
  • 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
  • Results manager
  • Results manager: introduction
  • Results: removing

    • s

  • Save list
  • Saving: contig editor
  • Screen only: assembly
  • Searching by annotation comments: contig editor
  • Searching by edits: 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
  • Select tags: template display
  • selecting contigs: Contig Selector
  • Selections: contig editor
  • Set Active Tags: contig editor
  • Set Output List: contig editor
  • Settings menu: contig editor
  • Shift readings: doctor database
  • Shifting readings: contig editor
  • Shotgun assembly
  • Show quality: contig editor
  • Show relationships
  • Show Strands: contig editor
  • Shuffle Pads: contig editor
  • Single stranded regions: assembling into
  • 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
  • Superedit: contig editor

    • t

  • Tag database
  • Tags
  • Tags: contig editor
  • Tags: restriction enzymes plot
  • Tags: template display
  • Template Display
  • Template display: active readings
  • 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: select tags
  • Template display: tags
  • Template Display: template plot
  • Template plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Tips on assembly
  • Toggle auto-save: contig editor
  • Trace displays: contig editor
  • Translations: contig editor

    • u

  • Unattached readings: lists
  • Unfinished consensus

    • v

  • Vector structure: doctor database
  • 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 29 April 1996.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_122.html