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Master Index

For version-1996.1

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

-

  • -maxdb
  • -maxseq
  • -read_only
    •

    .

  • .gaprc file
  • .pregaprc file
    •

    3

  • 3 Character Amino Acids: contig editor
    •

    a

  • abi_Ent_com: pregap variable
  • abi_Exp_com: pregap variable
  • abi_SCF_com: pregap variable
  • AC: experiment file line type
  • Active sequence: sip
  • Active tags
  • alf_Ent_com: pregap variable
  • alf_Exp_com: pregap variable
  • alf_SCF_com: pregap variable
  • Align sequences: sip
  • Align: contig editor
  • ALU, screening for using repe
  • Annotating contigs
  • Annotating readings
  • Annotation structure: doctor database
  • Annotations: contig editor
  • Annotations: deleting (Doctor Database)
  • Annotations: outputting to file (Doctor Database)
  • AP: experiment file line type
  • AQ: experiment file line type
  • Assemble: independently i.e. ignoring previous data
  • 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
  • Assembly
  • Auto-display Traces: contig editor
  • Auto-save: contig editor
  • AV: experiment file line type
    •

    b

  • Backing up databases
  • Bap databases: conversion to gap
  • Base accuracies - use of
  • Base: SCF structure
  • BC: experiment file line type
  • Boolean operations: sequence library browser
  • Break contig
  • Busy file
  • Buttons: mouse overview
  • Buttons
  • Byte ordering: SCF
    •

    c

  • Calculate consensus: algorithm
  • Calculate consensus: extended consensus
  • Calculate consensus: normal consensus
  • Calculate consensus: quality
  • Calculate consensus: unfinished consensus
  • Calculate consensus
  • CC: experiment file line type
  • CF: experiment file line type
  • CF: pregap variable
  • CF_com: pregap variable
  • CF_def: pregap variable
  • CH: experiment file line type
  • Changing the default number of matches: sip
  • Changing the maximum number of matches: sip
  • Changing the number of entries in list box: sequence library browser
  • Changing the score matrix: sip
  • Check assembly
  • 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
  • Check database
  • CL: experiment file line type
  • Clear: in output window
  • Clip: man page
  • Clip: pregap, use within
  • clip_args: pregap
  • Clone structure: doctor database
  • Cloning site, defining
  • Cloning site, finding
  • CN: experiment file line type
  • CN: pregap variable
  • CN_com: pregap variable
  • Colour blindness
  • Colour configuration window
  • Colour selector
  • Combining results: sequence library browser
  • Command line arguments: Trev
  • Command line arguments
  • Commands menu: contig editor
  • Comments: SCF
  • Compare Strands: contig editor
  • Complement sequence: sip
  • 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 example
  • Convert program
  • Copy list
  • CR: experiment file line type
  • Create list
  • Creating a new database
  • crosshairs: sip
  • CS: experiment file line type
  • Cut sites: restriction enzymes
  • Cutoff data: contig editor
  • Cutoff data: Trev
  • Cutoff values: contig editor
  • CV: experiment file line type
  • CV: pregap variable
  • CV_com: pregap variable
    •

    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
  • Delete sequence: sip
  • Deleting entrynames: sequence library browser
  • Deleting results: sequence library browser
  • Directed assembly
  • Directories: file browser
  • Disassemble readings
  • do_qual_clip: pregap variable
  • do_qual_clip_def: pregap variable
  • 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
  • Doctor Database
  • Dot plot: sip
  • Double strand
  • DR: experiment file line type
  • DR: pregap variable
  • DR_com: pregap variable
  • DT: experiment file line type
  • DT: pregap variable
  • DT_com: pregap example
  • DT_com: pregap variable
  • Dump Contig: contig editor
    •

    e

  • eba: man page
  • Eba: pregap, use within
  • Edit list
  • Editing and base accuracies
  • Editing modes: contig editor
  • Editing the sequence: Trev
  • Editing: contig editor
  • Editing: Trev
  • EN: experiment file line type
  • Enter pre-assembled data
  • Entering readings
  • Entering the search word: sequence library browser
  • Entry boxes
  • entry sequence: sip
  • Entrynames: sequence library browser
  • Error window
  • EX: experiment file line type
  • EX: pregap variable
  • EX_com: pregap variable
  • Example experiment file
  • expected number of matches in sip
  • Experiment file: example
  • Experiment file: explanation of records
  • Experiment file: unsupported additions
  • Experiment files: record types
  • Experiment files
  • Extended consensus
  • Extending structures: doctor database
  • extract_seq: man page
    •

    f

  • Fasta output from Gap
  • Field selection: sequence library browser
  • File browser: directories
  • File browser: files
  • File browser: filters
  • File browser: formats
  • File browser: introduction
  • File browser
  • File structure: SCF
  • file_type: pregap variable
  • file_type_def: pregap variable
  • Filebrowser: Trev
  • Files: file browser
  • Filters: file browser
  • Find best diagonals: sip
  • Find internal joins: dialogue
  • Find internal joins
  • Find matching words: sip
  • Find oligos
  • Find read pairs: display
  • Find read pairs: example
  • Find read pairs: output
  • Find read pairs: reading lines
  • Find read pairs: template lines
  • Find read pairs
  • Find repeats
  • Find similar spans: sip
  • FM: experiment file line type
  • fofn: pregap variable
  • fofn_def: pregap variable
  • format of protein score matrix
  • Formats: file browser
    •

    g

  • get_scf_field: man page
  • Graphics windows: user interface
  • GTAGDB
    •

    h

  • Header record: SCF
  • Header: SCF structure
  • Hidden data: contig editor
  • Hidden data
  • Highlight Disagreements: contig editor
  • Highlighting readings in the editor
    •

    i

  • ID: experiment file line type
  • identifying contigs
  • Ignore single templates: template display
  • Information: Trev
  • init_exp: man page
  • Init_exp: pregap, use within
  • Insertion and deletion of bases: contig editor
    •

    j

  • Join Editor
    •

    l

  • Labelling contigs
  • Labelling readings
  • LE: experiment file line type
  • Left mouse button: overview
  • LI: experiment file line type
  • Library selection: sequence library browser
  • Line thickness configuration
  • Listing the contents of a result: sequence library browser
  • Listing the contents of an entry: sequence library browser
  • Lists: commands
  • Lists: copy
  • Lists: create
  • Lists: delete
  • Lists: edit
  • Lists: introduction
  • Lists: load
  • Lists: minimal coverage
  • Lists: save
  • Lists: unattached readings
  • Lists
  • LN: experiment file line type
  • Load list
  • Long readings: suggestion of
  • LT: experiment file line type
    •

    m

  • Magic number: SCF
  • makeSCF: man page
  • MakeSCF: pregap, use within
  • Marking contigs
  • Masking contigs
  • match probabilities in sip
  • maxdb
  • maxseq
  • MC: experiment file line type
  • MC: pregap variable
  • MC_com: pregap variable
  • Menus
  • Middle mouse button: overview
  • minimal coverage: lists
  • MN: experiment file line type
  • MN: pregap variable
  • MN_com: pregap variable
  • Mouse buttons: overview
  • Mouse control: overview
  • MT: experiment file line type
  • MT_com: pregap example
    •

    n

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

    o

  • Oligo search
  • Oligo selection: contig editor
  • Oligos: choosing for probes
  • ON: experiment file line type
  • OP: experiment file line type
  • OP: pregap variable
  • OP_com: pregap example
  • OP_com: pregap variable
  • Opening a trace file: Trev
  • Opening databases
  • Operations on the Results: sequence library browser
  • Options menu
  • Output annotations to file
  • Output window
    •

    p

  • Pads: contig editor
  • PC: experiment file line type
  • Performing the search: sequence library browser
  • Permanent results: sip
  • personal file entry: sip
  • pln_Ent_com: pregap variable
  • pln_Exp_com: pregap variable
  • Plot stop codons: examining the plot
  • Plot stop codons: updating the plot
  • Plot stop codons
  • PN: experiment file line type
  • PN: pregap variable
  • PN_com: pregap variable
  • PR: experiment file line type
  • PR: pregap variable
  • PR_com: pregap variable
  • Preassembled data: assembly
  • Pregap: automation
  • Pregap: clip
  • Pregap: clip_args
  • Pregap: configuration
  • Pregap: eba
  • Pregap: Example integration - full database
  • Pregap: Example integration - simple database
  • Pregap: Example integration - squirrel database
  • Pregap: init_exp
  • Pregap: integration
  • Pregap: interaction
  • Pregap: introduction
  • Pregap: makeSCF
  • Pregap: notes
  • Pregap: processes
  • Pregap: questions
  • Pregap: repe
  • Pregap: squirrel database
  • Pregap: summary
  • Pregap: trev
  • Pregap: trev_args
  • pregap: variable list
  • Pregap: vepe
  • pregaprc file
  • Primer Selection: contig editor
  • Primer site, defining
  • Primer site, finding (in full)
  • Primer site, finding forward site quickly
  • Primer site, finding forward site
  • Primer site, finding quickly
  • Primer site, finding reverse site quickly
  • Primer site, finding reverse site
  • Primers: suggestion of
  • Private data: SCF
  • probabilities in sip
  • protein score matrix format
  • PS: experiment file line type
    •

    q

  • QL: experiment file line type
  • QR: experiment file line type
  • qual_clip_interactive: pregap variable
  • qual_clip_interactive_def: pregap variable
  • Quality calculation
  • Quality codes
  • Quality plot: template display
  • Quality values: contig editor, displayed
  • Quality values: contig editor, use within
  • Quality: output for consensus
  • Quit: Trev
  • Quitting: contig editor
    •

    r

  • Read pairs
  • read sequence: sip
  • read_only
  • Reading names
  • Reading numbers
  • Reading plot: template display
  • Reading structure: doctor database
  • Readings list: template display
  • Records in experiment files
  • Redirect output
  • Redisplaying temporary results: sip
  • Removing readings
  • Removing results
  • Repe: error codes
  • Repe: pregap, use within
  • Repe: searching for other repeats
  • Repe
  • repe_repeat_file: pregap variable
  • repe_tag_type: pregap variable
  • Repeat search
  • Repeats, screening for using repe
  • Restriction enzyme files
  • Restriction enzymes: configuring
  • Restriction enzymes: cut sites
  • Restriction enzymes: examining the plot
  • Restriction enzymes: introduction
  • Restriction enzymes: screening
  • Restriction enzymes: selecting enzymes
  • Restriction enzymes: tags, creation of
  • Restriction enzymes: template display
  • Results manager: introduction
  • results manager: sip
  • Results manager
  • Results: removing
  • Results: sequence library browser
  • Right mouse button: overview
    •

    s

  • Sample points: SCF
  • Samples1: SCF structure
  • Samples2: SCF structure
  • Save list
  • Save sequence: sip
  • Save: sequence library browser
  • Saving: contig editor
  • Saving: Trev
  • SC: experiment file line type
  • SC: pregap variable
  • SC_com: pregap variable
  • SC_def: pregap variable
  • Scale_trace_clip: man page
  • Scaling: Trev
  • SCF header record
  • SCF magic number
  • SCF: byte ordering
  • SCF: comments
  • SCF: file structure
  • SCF: private data
  • SCF: Sample points
  • SCF: sequence
  • SCF
  • scf_Exp_com: pregap variable
  • score matrix format
  • Scramble sequence: sip
  • Screen only: assembly
  • screen_av: pregap variable
  • screen_av_def: pregap variable
  • screen_cv: pregap variable
  • screen_cv_def: pregap variable
  • screen_sv: pregap variable
  • screen_sv_def: pregap variable
  • Screening against Restriction Enzymes
  • Screening against vector sequence
  • Screening readings for repeat families
  • Scroll on output
  • SE: experiment file line type
  • Search mode: sequence library browser
  • 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
  • Searching: Trev
  • Select tags: template display
  • Select Tags
  • Selecting an entryname or accession number for the parent program: sequence library browser
  • selecting contigs: Contig Selector
  • Selecting the output parameters: sequence library browser
  • Selections: contig editor
  • Sequence display: sip
  • sequence library browser: Changing the number of entries in list box
  • sequence library browser: Combining results
  • sequence library browser: Deleting entrynames
  • sequence library browser: Deleting results
  • sequence library browser: entering the search word
  • sequence library browser: Entrynames
  • sequence library browser: field selection
  • sequence library browser: library selection
  • sequence library browser: Listing the contents of a result
  • sequence library browser: Listing the contents of an entry
  • sequence library browser: Operations on the Results
  • sequence library browser: performing the search
  • sequence library browser: results
  • sequence library browser: Save
  • sequence library browser: search mode
  • sequence library browser: Selecting an entryname or accession number for the parent program
  • sequence library browser: Selecting the output parameters
  • sequence library entry: sip
  • Sequence manager: sip
  • Sequence: SCF
  • Set Active Tags: contig editor
  • Set Output List: contig editor
  • setting parameters for trace_clip
  • Settings menu: contig editor
  • SF: experiment file line type
  • SF: pregap variable
  • SF_com: pregap variable
  • SF_def: pregap variable
  • Shift readings: doctor database
  • Shifting readings: contig editor
  • Shotgun assembly
  • Show quality: contig editor
  • Show relationships
  • Show Strands: contig editor
  • Shuffle Pads: contig editor
  • SI: experiment file line type
  • SI: pregap variable
  • SI_com: pregap variable
  • significance of matches in sip
  • Single stranded regions: assembling into
  • Sip plot: sip
  • sip: active sequence
  • sip: Align sequences
  • sip: Calculating the expected number of matches
  • sip: Changing the default number of matches
  • sip: Changing the maximum number of matches
  • sip: Changing the score matrix
  • sip: complement sequence
  • sip: crosshairs
  • sip: delete sequence
  • sip: dot plot
  • sip: Expected numbers of matches
  • sip: Find best diagonals
  • sip: Find matching words
  • sip: Find similar spans
  • sip: match probabilities
  • sip: permanent results
  • sip: personal file entry
  • sip: reading in sequences
  • sip: redisplaying temporary results
  • sip: results manager
  • sip: save sequence
  • sip: scramble sequence
  • sip: Sequence display
  • sip: sequence library entry
  • sip: sequence manager
  • sip: significance of matches
  • sip: sip plot
  • sip: temporary results
  • sip: translate sequence
  • sip: zoom
  • SL: experiment file line type
  • SP: experiment file line type
  • SP: pregap variable
  • SP_com: pregap variable
  • SP_def: pregap variable
  • SQ: experiment file line type
  • Squirrel: using with pregap
  • SR: experiment file line type
  • SS: experiment file line type
  • SS: pregap variable
  • SS_com: pregap variable
  • ST: experiment file line type
  • ST: pregap variable
  • ST_com: pregap variable
  • 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
  • SV: experiment file line type
  • SV: pregap variable
  • SV_com: pregap variable
  • system-pregaprc file
    •

    t

  • Tag database
  • Tag selector
  • tag_alu: pregap variable
  • tag_alu_def: pregap variable
  • Tags: contig editor
  • Tags: restriction enzymes plot
  • Tags: template display
  • Tags
  • TC: experiment file line type
  • 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 Display
  • Template plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Temporary results: sip
  • Text windows
  • TG: experiment file line type
  • Tips on assembly
  • TN: experiment file line type
  • TN: pregap variable
  • TN_com: pregap variable
  • Toggle auto-save: contig editor
  • Trace displays: contig editor
  • trace_clip parameter setting
  • Trace_clip: man page
  • Translate sequence: sip
  • Translations: contig editor
  • Trev: editing the sequence
  • Trev: editing
  • Trev: information
  • Trev: introduction
  • Trev: opening a trace file
  • Trev: pregap, use within
  • Trev: quit
  • Trev: saving a trace file
  • Trev: scaling
  • Trev: searching
  • Trev: setting cutoffs
  • Trev
  • trev_args: pregap
    •

    u

  • Unattached readings: lists
  • Unfinished consensus
  • User interface: buttons
  • User interface: colour selector
  • User interface: entry boxes
  • User interface: introduction
  • User interface: menus
  • User interface: tag selector
  • User interface: text windows
  • User interface: Zooming graphics
  • User interface
    •

    v

  • Vector sequence: screening
  • Vector structure: doctor database
  • Vepe: cloning site, defining
  • Vepe: error codes
  • Vepe: finding primer site (in full)
  • Vepe: finding primer site - forward
  • Vepe: finding primer site - reverse
  • Vepe: finding primer site quickly - forward
  • Vepe: finding primer site quickly - reverse
  • Vepe: finding primer site quickly
  • Vepe: pregap, use within
  • Vepe: primer site, defining
  • Vepe
  • vepe_avec_min_match: pregap variable
  • vepe_cvec_diagonals: pregap variable
  • vepe_cvec_score: pregap variable
  • vepe_cvec_word_length: pregap variable
  • vepe_svec_diagonals: pregap variable
  • vepe_svec_score: pregap variable
  • vepe_svec_word_length: pregap variable
  • Verfiy AND: contig editor
  • Verfiy OR: contig editor
  • View menu: Contig Selector
    •

    z

  • zoom: sip
  • Zooming graphics
    •
    home brief full
    This document was generated using the merge_indexes.pl program.

    This page is maintained by James Bonfield. Last generated on 29 April 1996.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/master_index.html