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Master Index

For version-1999.0

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

-

  • --
  • -check
  • -config
  • -fofn
  • -maxdb
  • -maxseq
  • -no_exec_notes
  • -no_rawdata_note
  • -no_win
  • -nocheck
  • -nowin
  • -read_only
  • -win_compact
  • -win_separate
  • .

  • .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 file
  • .log
  • .passed
  • .phrap_log
  • .pregap4rc
  • .pregaprc file
  • .report
  • .scf_dir
  • .screenseq_failed
  • .screenseq_passed
  • .screenvec_failed
  • .screenvec_passed
  • .seqlibrc: sequence library browser
  • .singlets
  • .svec_failed
  • .svec_passed
  • .tagrep_free
  • .tagrep_log
  • .tagrep_repeat
  • 3

  • 3 Character Amino Acids: contig editor
  • _

  • _com
  • a

  • abi_Ent_com: pregap variable
  • abi_Exp_com: pregap variable
  • abi_filenames
  • abi_samplenames
  • abi_SCF_com: pregap variable
  • ABI_use_sample_name
  • AC: experiment file line type
  • Active sequence: nip
  • Active sequence: sip
  • Active tags
  • Adding modules
  • ALF/ABI to SCF conversion configuration
  • ALF/ABI to SCF conversion module
  • alf_Ent_com: pregap variable
  • alf_Exp_com: pregap variable
  • alf_SCF_com: pregap variable
  • Align sequences: sip
  • Align: contig editor
  • aligning pads: contig editor
  • Alignment local: sip
  • 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
  • ALU, screening for using repe
  • alu_only
  • Amino acid composition:nip
  • Annotating contigs
  • Annotating readings
  • Annotation Selector
  • Annotation structure: doctor database
  • Annotations: contig editor
  • Annotations: deleting (Doctor Database)
  • Annotations: outputting to file (Doctor Database)
  • AP: experiment file line type
  • AP: pregap variable
  • AP_com: pregap variable
  • AQ: experiment file line type
  • Arguments, command line
  • assem_d_threshold
  • assem_e_rate
  • assem_number
  • assem_o_threshold
  • Assemble: independently i.e. ignoring previous data
  • Assembly: CAP2
  • Assembly: CAP3 information
  • Assembly: CAP3
  • 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
  • Assembly
  • Augment Experiment files configuration
  • Augment Experiment files module
  • Augment, by line types
  • Augment, by text database
  • augment_exp.p4m
  • Author test:nip
  • Auto-display Traces: contig editor
  • Auto-save: contig editor
  • AV: experiment file line type
  • b

  • Backing up databases
  • band_width
  • Bap databases: conversion to gap
  • Base accuracies - use of
  • Base composition plotting:nip
  • Base composition:nip
  • Base: SCF structure
  • BASE_BRIEF_FORMAT1
  • BASE_BRIEF_FORMAT2
  • Batch mode
  • BC: experiment file line type
  • bit_size
  • Blast screen configuration
  • Blast screen module
  • blast.p4m
  • Boolean operations: sequence library browser
  • Break contig: contig editor
  • Break contig
  • Busy file
  • Buttons: mouse overview
  • Buttons
  • Byte ordering: SCF
  • c

  • Calculate consensus: algorithm
  • Calculate consensus: confidence
  • Calculate consensus: extended consensus
  • Calculate consensus: normal consensus
  • Calculate consensus: quality
  • Calculate consensus: reliability
  • Calculate consensus: unfinished consensus
  • Calculate consensus
  • Cap2 assembly configuration
  • Cap2 assembly module
  • CAP2 assembly: import
  • CAP2 assembly: perform and import
  • CAP2 assembly: perform
  • CAP2 assembly: stand alone
  • CAP2 Assembly
  • cap2_assemble.p4m
  • Cap3 assembly configuration
  • Cap3 assembly module
  • CAP3 assembly: import
  • CAP3 assembly: information
  • CAP3 assembly: perform and import
  • CAP3 assembly: perform
  • CAP3 assembly: stand alone
  • CAP3 Assembly
  • cap3_assemble.p4m
  • CC: experiment file line type
  • CF: experiment file line type
  • CF: pregap variable
  • CF
  • CF_com: pregap variable
  • CF_def: pregap variable
  • CH: experiment file line type
  • CH: pregap_variable
  • CH_com: pregap_variable
  • Changing default library: sequence library browser
  • 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 (command line option)
  • Check assembly
  • 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
  • Check database
  • check_params
  • Circular sequence:nip
  • CL: experiment file line type
  • Clear: in output window
  • Clip: man page
  • Clip: pregap, use within
  • clip_args: pregap
  • clip_args
  • Clipping by differences
  • Clipping by quality
  • clipping readings
  • Clipping within Gap4
  • clipping: pregap
  • Clone structure: doctor database
  • Cloning site, defining
  • Cloning site, finding
  • Cloning vector clip configuration (old style)
  • Cloning vector clip configuration
  • Cloning vector clip module (old style)
  • Cloning vector clip module
  • cloning_vector_clip.p4m
  • CLOS note type
  • Cloverleaf:nip
  • CN: experiment file line type
  • CN: pregap variable
  • CN_com: pregap variable
  • Codon composition:nip
  • Codon frequencies:nip
  • Codon tables:nip
  • Codon usage method:nip
  • Codon usage tables:nip
  • Codon usage:nip
  • Colour blindness
  • Colour configuration window
  • Colour selector
  • Colour: contig editor highlight disagreements
  • Colours
  • Combining results: sequence library browser
  • Command line arguments: Trev
  • Command line arguments
  • Command line arguments
  • Commands menu: contig editor
  • Comments: SCF
  • Communication
  • Comparator window
  • Compare Strands: contig editor
  • Complement contig
  • Complement sequence: nip
  • Complement sequence: sip
  • Component configuration
  • Components
  • Composition of protein sequence:nip
  • Composition: sequence:nip
  • Compress Trace Files configuration
  • Compress Trace Files module
  • compress_trace.p4m
  • compression
  • Compressions: suggested experiments
  • Confidence in contig editor
  • Confidence of consensus
  • Confidence values - use of
  • Confidence values: editing techniques
  • Configuration files
  • Configuration, manual
  • Configure Cutoffs
  • Configure: restriction enzymes: nip
  • Configure: restriction enzymes
  • configure_dialogue
  • Configuring modules
  • Configuring pregap4
  • Configuring: fonts
  • Configuring: sequence library browser
  • Consensus calculation confidence
  • Consensus calculation method
  • Consensus: outputting
  • Conserved bases in tRNA:nip
  • Contig comparator: auto navigation
  • Contig Comparator: manipulating results
  • Contig comparator: next button
  • Contig Comparator
  • 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 movement
  • Contig Editor: cursor
  • 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 menu
  • Contig Editor: trace display
  • 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 example
  • Convert program
  • Copy Database
  • Copy list
  • Copy_db: man page
  • CR: experiment file line type
  • Create list
  • create
  • create_dialogue
  • Creating a new database
  • Cross_match configuration
  • Cross_match module
  • cross_match_svec.p4m
  • Crosshairs: nip
  • Crosshairs: sip
  • CS: experiment file line type
  • Cursor dragging:nip
  • Cursor linking:nip
  • Cursor positioning:nip
  • Cursor: contig editor
  • Cursor: nip
  • Cursor: sip
  • Cut sites: restriction enzymes
  • Cutoff data: contig editor
  • Cutoff data: Trev
  • cutoff score: trace_diff
  • Cutoff values: contig editor
  • cutoff
  • Cutting sites: restriction enzymes:nip
  • CV: experiment file line type
  • CV: pregap variable
  • CV_com: pregap variable
  • d

  • Dap databases: conversion to bap or gap
  • data hidden
  • Database integration
  • Database merging
  • Database splitting
  • Database structure: doctor database
  • Database, plain text format
  • Database: backups
  • Database: busy file
  • Database: creating new
  • Database: gap filenames
  • Database: new
  • Database: opening
  • database_name
  • database_version
  • def_5_pos
  • Delete annotations
  • Delete contig: doctor database
  • Delete list
  • Delete sequence: nip
  • Delete sequence: sip
  • Deleting entrynames: sequence library browser
  • Deleting results: sequence library browser
  • detection of mutations: introduction
  • diag_score
  • Diff against consensus trace: contig editor
  • Diff against specific trace: contig editor
  • Difference clipping
  • difference_clip
  • Dinucleotide frequencies:nip
  • Directed assembly
  • Directories: file browser
  • Directories
  • Disassemble readings
  • Disassembly: contig editor
  • Discrepancies: searching for in contig editor
  • Display interaction:nip
  • DNA character set
  • DNA translation:nip
  • 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: note structure
  • Doctor database: original clone structure
  • Doctor database: reading structure
  • Doctor database: reset contig order
  • Doctor database: shift readings
  • Doctor database: template structure
  • Doctor Database
  • Dot plot: sip
  • Dots: contig editor highlight disagreements
  • Double strand
  • Double stranded sequence listing:nip
  • DR: experiment file line type
  • DR: pregap variable
  • DR_com: pregap variable
  • Drag and drop graphics: nip
  • Drag and drop graphics: sip
  • DT: experiment file line type
  • DT: pregap variable
  • DT_com: pregap example
  • DT_com: pregap variable
  • Dump Contig: contig editor
  • Dumping results to file:nip
  • Duplicate matches: sip
  • e

  • eba.p4m
  • eba: man page
  • Eba: pregap, use within
  • 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: confidence values
  • Editing techniques: overcalls
  • Editing techniques
  • Editing the sequence: Trev
  • Editing: contig editor
  • Editing: Trev
  • Email configuration
  • Email module
  • email.p4m
  • email_address
  • email_args
  • email_progam
  • EN: experiment file line type
  • enabled
  • end
  • Enter assembly configuration
  • Enter assembly module
  • Enter pre-assembled data
  • enter_all
  • enter_assembly.p4m
  • Entering readings
  • Entering the search word: sequence library browser
  • Entry boxes
  • Entry sequence: sip
  • Entrynames: sequence library browser
  • error codes in screen_seq
  • error codes in vector_clip
  • error messages: find internal joins
  • error messages: maxseq
  • Error window
  • Estimate base accuracies configuration
  • Estimate base accuracies module
  • Evidence for Edit1: contig editor
  • Evidence for Edit2: contig editor
  • EX: experiment file line type
  • EX: pregap variable
  • EX_com: pregap variable
  • Example code
  • Example experiment file
  • Expected number of matches in sip
  • Experiment File line types
  • Experiment file name length restrictions
  • Experiment file name restrictions
  • Experiment file name restrictions
  • 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
  • extraneous readings: filtering out
  • f

  • FakII assembly configuration
  • FakII assembly module
  • FAKII assembly: import
  • FAKII assembly: perform and import
  • FAKII assembly: perform
  • FAKII Assembly
  • fakii_assemble.p4m
  • FAQ
  • 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 formats for vectors
  • file location: trace file location
  • File menu: Contig Selector
  • File name restrictions
  • File name restrictions
  • File of filenames generation
  • File structure: SCF
  • file_error
  • file_id
  • file_type: pregap variable
  • file_type
  • file_type_def: pregap variable
  • Filebrowser: Trev
  • Files, specifying
  • Files: file browser
  • filtering out extraneous readings
  • Filters: file browser
  • Find best diagonals: sip
  • Find internal joins: dialogue
  • Find internal joins
  • Find matching words: sip
  • Find oligos
  • Find open reading frames:nip
  • 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
  • Finding genes: Introduction:nip
  • finding joins
  • finding overlaps
  • Finding protein genes:nip
  • Finding strings:nip
  • FM: experiment file line type
  • fofn: pregap variable
  • fofn_def: pregap variable
  • Fonts, within trev
  • Fonts
  • Fonts
  • Fonts
  • Format of protein score matrix
  • format: vector_primer files
  • Formats: file browser
  • formats: vector files
  • Frequently asked questions
  • Functions, builtin
  • Functions, in modules
  • g

  • Gap4 and Nip4 communication
  • Gap4 shotgun assembly configuration
  • Gap4 shotgun assembly module
  • gap4: checking predicted mutations
  • gap4: mutation checking
  • gap4: mutation detection
  • gap4_assemble.p4m
  • Gene finding: Introduction:nip
  • General configuration configuration
  • General configuration module
  • generate_constraints
  • Genetic code:nip
  • Get sequence: nip
  • Get sequence: sip
  • get_scf_field: man page
  • Global variables
  • Goto file button, trev
  • graph_d_limit
  • graph_e_limit
  • graph_o_threshold
  • Graphics rearrangement: nip
  • Graphics rearrangement: sip
  • Graphics windows: user interface
  • Green, Phil (Phrap)
  • Group Readings by Templates: contig editor
  • GTAGDB
  • h

  • Header record: SCF
  • Header: SCF structure
  • Hidden data: contig editor
  • Hidden data
  • hidden data
  • hidden data
  • hidden
  • Hide duplicate matches: sip
  • Hide, in Contig Comparator
  • Highlight Disagreements: contig editor
  • Highlighting readings in the editor
  • Huang: Assembly (CAP2)
  • Huang: Assembly (CAP3)
  • i

  • ID: experiment file line type
  • 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 sources
  • Information, in Contig Comparator
  • Information: Trev
  • init.p4m
  • init
  • init_exp.p4m
  • init_exp: man page
  • Init_exp: pregap, use within
  • Initialise Experiment files configuration
  • Initialise Experiment files module
  • Interaction of displays:nip
  • Interactive clipping configuration
  • Interactive clipping module
  • interactive_clip.p4m
  • Interconvert t and u: nip
  • Interconvert t and u: sip
  • Introduction
  • Intron in tRNA:nip
  • Intron/exon boundaries:nip
  • Invoke contig editors, in Contig Comparator
  • Invoke contig join editors, in Contig Comparator
  • Invoke template display, in Contig Comparator
  • j

  • Join Editor
  • joining contigs
  • k

  • keep_names
  • l

  • Labelling contigs
  • Labelling readings
  • LE: experiment file line type
  • Left mouse button: overview
  • left_num_uncalled
  • left_win_length
  • LI: experiment file line type
  • Library search: nip
  • Library search: sip
  • Library selection: sequence library browser
  • library
  • Line thickness configuration
  • Line types, in experiment file
  • Linear sequence:nip
  • List confidence: contig editor
  • List confidence
  • Listbox
  • Listing the contents of a result: sequence library browser
  • Listing the contents of an entry: sequence library browser
  • 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
  • Lists
  • LN: experiment file line type
  • Load list
  • Load sequence: nip
  • Load sequence: sip
  • Local alignment: sip
  • Long readings: suggestion of
  • LT: experiment file line type
  • m

  • Magic number: SCF
  • makeSCF: man page
  • MakeSCF: pregap, use within
  • mandatory
  • Manual configuration
  • Marking contigs
  • marking
  • Masking contigs
  • masking
  • Match probabilities in sip
  • match_fraction
  • Matching strings:nip
  • max_extent
  • max_length
  • max_pads
  • max_pmismatch
  • max_right
  • maxdb (command line option)
  • maxseq (command line option)
  • maxseq: find internal joins
  • Maxseq
  • MC: experiment file line type
  • MC: pregap variable
  • MC_com: pregap variable
  • Memory saving: nip
  • Memory saving:nip
  • Memory usage:nip
  • Menus
  • Merging databases
  • Middle mouse button: overview
  • min_3_match
  • min_5_match
  • min_extend
  • min_left
  • min_match
  • minimal coverage: lists
  • minmatch
  • minscore
  • MN: experiment file line type
  • MN: pregap variable
  • MN_com: pregap variable
  • Mode sets: contig editor
  • Module functions
  • Module variables
  • Module, example code
  • MODULE_PATH
  • Modules, adding and removing
  • Modules, configuring
  • Modules, creating
  • Modules, overview
  • MODULES
  • Motif searching: percentage matches:nip
  • Mouse buttons: overview
  • Mouse control: overview
  • MT: experiment file line type
  • MT_com: pregap example
  • Multiple files in Trev
  • mutation checking in gap4
  • mutation cutoff score
  • Mutation detection configuration
  • Mutation detection module
  • Mutation detection: introduction
  • mutation detection: searching
  • mutation threshold
  • Myers: Assembly (FAKII)
  • n

  • name
  • names in the editor
  • naming contigs
  • Naming conventions
  • Naming schemes, creating.
  • Naming schemes
  • NC-IUB symbols:nip
  • netscape
  • New database creation
  • Next button, in Contig comparator
  • Next button, trev
  • Nip plot: nip
  • Nip4 and Gap4 communication
  • no_low_complexity
  • no_primate_rodent
  • nocheck (command line option)
  • Non-interactive processing
  • Normal consensus
  • normal mode (trace display): contig editor
  • Normalisation: codon usage tables:nip
  • Note structure: doctor database
  • Notes: editing
  • Notes: introduction
  • Notes: selecting
  • Notes: special types
  • Notes
  • Nucleotide symbols
  • num_diags
  • o

  • offset
  • Old cloning vector clip configuration
  • old_cloning_vector_clip.p4m
  • Oligo search
  • Oligo searching:nip
  • 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
  • OPEN note type
  • Open reading frames:nip
  • Opening a trace file: Trev
  • Opening databases
  • Operations on the Results: sequence library browser
  • Options menu
  • Ordering contigs:gap4
  • other_args
  • Output annotations to file
  • Output enzyme by enzyme: restriction enzymes plot
  • Output ordered on position: restriction enzymes plot
  • Output window
  • Overcalls: editing techniques
  • overlap finding
  • p

  • pad alignment: contig editor
  • pad shuffling: contig editor
  • path for trace files: RAWDATA
  • PC: experiment file line type
  • PD: primer data - the sequence of a primer
  • Percentage matches:nip
  • Performing the search: sequence library browser
  • Permanent results: sip
  • Persistence of results:nip
  • Personal search: nip
  • Personal search: sip
  • Phrap assembly configuration
  • Phrap assembly module
  • Phrap Assembly
  • phrap_assemble.p4m
  • Phred configuration
  • Phred module
  • phred.log
  • phred.p4m
  • 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
  • Plotting base composition:nip
  • PN: experiment file line type
  • PN: pregap variable
  • PN_com: pregap variable
  • Positional base preferences:nip
  • PR: experiment file line type
  • PR: pregap variable
  • PR_com: pregap variable
  • Preassembled data: assembly
  • pregap4.config
  • pregap4rc
  • 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: naming conventions
  • Pregap: notes
  • Pregap: processes
  • Pregap: quality clipping
  • Pregap: questions
  • Pregap: repe
  • Pregap: squirrel database
  • Pregap: summary
  • Pregap: trev
  • Pregap: trev_args
  • pregap: variable list
  • Pregap: vector_clip
  • pregaprc file
  • Previous button, trev
  • Primer selection: contig editor
  • Primer Selection: contig editor
  • Primer site, defining
  • Primer site, finding
  • Primers: suggestion of
  • Print list
  • Private data: SCF
  • Probabilities in sip
  • probability
  • process_dialogue
  • Protein score matrix format
  • Protein sequence composition:nip
  • Protein:nip
  • PS: experiment file line type
  • q

  • QL: experiment file line type
  • QL_def: pregap variable
  • QR: experiment file line type
  • QR_def: pregap variable
  • qual_clip_interactive: pregap variable
  • qual_clip_interactive_def: pregap variable
  • Quality calculation
  • quality clipping: pregap
  • 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
  • quality_clip
  • Quit: Trev
  • Quitting: contig editor
  • r

  • Range: sip
  • Range:nip
  • RAWD note type
  • RAWDATA: trace file location
  • Read pair data and contig ordering
  • Read pairs
  • Read sequence: nip
  • Read sequence: sip
  • READ_BRIEF_FORMAT
  • read_only (command line option)
  • reading clipping
  • Reading frame:nip
  • Reading name length restrictions
  • Reading name restrictions
  • Reading name restrictions
  • reading names in the editor
  • Reading names
  • Reading numbers
  • Reading plot: template display
  • Reading structure: doctor database
  • Readings list: template display
  • readings list
  • readings: entering
  • readings: extraneous
  • Records in experiment files
  • Redirect output
  • reference trace: trace_diff
  • Reject button, trev
  • Remove reading: contig editor
  • Remove, in Contig Comparator
  • removing extraneous readings
  • Removing modules
  • 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
  • repeat_file
  • repeat_masker.p4m
  • RepeatMasker configuration
  • RepeatMasker module
  • Repeats, screening for using repe
  • repeats_masker.p4m
  • report
  • Restriction enzyme files
  • Restriction enzyme sites:nip
  • Restriction enzymes: configuring: nip
  • Restriction enzymes: configuring
  • Restriction enzymes: cut sites
  • Restriction enzymes: examining the plot: nip
  • Restriction enzymes: examining the plot
  • Restriction enzymes: introduction: nip
  • Restriction enzymes: introduction
  • Restriction enzymes: selecting enzymes: nip
  • Restriction enzymes: selecting enzymes
  • Restriction enzymes: tags, creation of
  • Restriction enzymes: template display
  • Restriction enzymes: textual output
  • Restriction site listing:nip
  • Restriction site printing:nip
  • Restrictions on experiment file names
  • Restrictions on file names
  • Restrictions on reading names
  • Restrictions on sample names
  • Restrictions on SCF file names
  • Results manager: introduction
  • Results manager: nip
  • Results manager: sip
  • Results manager
  • Results menu: Contig Selector
  • Results: removing
  • Results: sequence library browser
  • Right mouse button: overview
  • right_num_uncalled
  • right_win_length
  • Rotate sequence: nip
  • Rotate sequence: sip
  • Ruler: template display
  • Run command
  • run
  • s

  • sample name restrictions
  • Sample name restrictions
  • Sample points: SCF
  • Samples1: SCF structure
  • Samples2: SCF structure
  • Sanger Centre naming scheme, new
  • Sanger Centre naming scheme, old
  • sanger_names_new.p4t
  • sanger_names_old.p4t
  • Save As
  • Save Consensus Trace: contig editor
  • Save list
  • Save sequence: nip
  • Save sequence: sip
  • Save: sequence library browser
  • Saving: contig editor
  • Saving: Trev
  • SC: experiment file line type
  • SC: pregap variable
  • SC
  • SC_com: pregap variable
  • SC_def: pregap variable
  • Scale_trace_clip: man page
  • Scaling: Trev
  • SCF file name restrictions
  • SCF file name restrictions
  • 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
  • SCF_use_sample_name
  • Score matrix format
  • score
  • Scramble sequence: nip
  • Scramble sequence: sip
  • Screen for unclipped vector configuration
  • Screen for unclipped vector module
  • Screen only: assembly
  • Screen sequences configuration
  • Screen sequences module
  • screen_av: pregap variable
  • screen_av_def: pregap variable
  • screen_cv: pregap variable
  • screen_cv_def: pregap variable
  • screen_file
  • screen_mode
  • screen_seq, limits
  • screen_seq.p4m
  • Screen_seq: error codes
  • Screen_seq: error codes
  • screen_seq: man page
  • Screen_seq
  • screen_seq
  • screen_sv: pregap variable
  • screen_sv_def: pregap variable
  • screen_vector.p4m
  • Screening against vector sequence
  • screening for bacterial sequences
  • screening for vectors
  • Screening readings for contaminant sequences
  • Screening readings for repeat families
  • Scroll on output
  • SE: experiment file line type
  • Search mode: sequence library browser
  • Search: in the output window
  • 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 for mutations
  • Searching for oligos:nip
  • Searching for strings:nip
  • Searching reading name: contig editor
  • Searching: contig editor
  • Searching: open reading frames:nip
  • Searching: protein genes:nip
  • Searching: splice sites:nip
  • Searching: start codons:nip
  • Searching: stop codons:nip
  • Searching: Trev
  • Searching: tRNA genes:nip
  • Select tags: template display
  • Selecting a sequence: nip
  • Selecting a sequence: sip
  • 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
  • Send To
  • Seq identifier: nip
  • Seq identifier: sip
  • Sequence composition:nip
  • Sequence deletion: nip
  • Sequence display: sip
  • Sequence display:nip
  • Sequence interpretation: finding protein genes:nip
  • Sequence interpretation: tRNA gene search:nip
  • sequence library browser: .seqlibrc
  • sequence library browser: Changing default library
  • sequence library browser: Changing the number of entries in list box
  • sequence library browser: Combining results
  • sequence library browser: Configuring
  • 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 manager: nip
  • Sequence manager: sip
  • Sequence reading: nip
  • Sequence scrolling:nip
  • Sequence type:nip
  • Sequence viewer:nip
  • Sequence: SCF
  • sequence_vector_clip.p4m
  • Sequencing vector clip configuration
  • Sequencing vector clip module
  • Set Active Tags: contig editor
  • Set Default Confidences: contig editor
  • Set Fonts
  • Set genetic code:nip
  • Set maxseq
  • Set Output List: contig editor
  • Set the range: sip
  • Set the range:nip
  • setting parameters for trace_clip
  • Settings menu: contig editor
  • SF: experiment file line type
  • SF: pregap variable
  • SF
  • SF_com: pregap variable
  • SF_def: pregap variable
  • 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
  • Shutdown configuration
  • shutdown.p4m
  • shutdown
  • SI: experiment file line type
  • SI: pregap variable
  • SI_com: pregap variable
  • Significance of matches in sip
  • Sim: sip
  • Simple search: nip
  • Simple search: sip
  • Simple Text Database
  • simple_only
  • Single stranded regions: assembling into
  • Single stranded sequence listing:nip
  • Sip plot: sip
  • Sites: restriction enzymes:nip
  • SL: experiment file line type
  • Smith-Waterman: sip
  • Sort Matches
  • SP: experiment file line type
  • SP: pregap variable
  • SP
  • SP_com: pregap variable
  • SP_def: pregap variable
  • Splice junctions:nip
  • Splice sites:nip
  • Splitting databases
  • 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
  • Start codons:nip
  • start
  • Status line: contig editor
  • Stems and loops:nip
  • Stop codons display
  • Stop codons: examining the plot
  • Stop codons: updating the plot
  • Stop codons:nip
  • Stops: suggested experiments
  • String finding:nip
  • String matching:nip
  • String searching:nip
  • Styles of windows
  • Suggest long readings
  • Suggest primers
  • Suggest probes
  • Summary of editing commands: contig editor
  • Summary: contig editor
  • Super contigs
  • Superedit: contig editor
  • SV: experiment file line type
  • SV: pregap variable
  • SV_com: pregap variable
  • system-pregaprc file
  • t

  • Tag database
  • Tag repeats configuration
  • Tag repeats module
  • Tag Selector
  • tag_alu: pregap variable
  • tag_alu_def: pregap variable
  • TAG_BRIEF_FORMAT
  • tag_repeats.p4m
  • tag_type
  • tag_types
  • Tags: contig editor
  • Tags: restriction enzymes plot
  • Tags: template display
  • Tags
  • TC: experiment file line type
  • Techniques of editing
  • 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 Display
  • Template plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Templates: grouping readings in contig editor
  • Temporary results: sip
  • Text windows
  • TG: experiment file line type
  • threshold: mutation detection
  • Tips on assembly
  • TN: experiment file line type
  • TN: pregap variable
  • TN_com: pregap variable
  • to_scf.p4m
  • Toggle auto-save: contig editor
  • Trace clipping
  • Trace Display menu: contig editor
  • Trace displays: contig editor
  • Trace displays: RAWDATA
  • Trace displays: trace file location
  • Trace quality clip configuration
  • Trace quality clip module
  • trace: reference
  • trace_clip parameter setting
  • trace_clip parameters: selecting
  • trace_clip.p4m
  • Trace_clip: man page
  • trace_diff.p4m
  • trace_diff: checking mutations in gap4
  • trace_diff: checking results in gap4
  • trace_diff: cutoff score
  • trace_diff: man page
  • trace_diff: producing a reference trace
  • trace_diff: producing a wild type trace
  • trace_diff: using
  • Transcribe sequence: nip
  • Transcribe sequence: sip
  • Translate sequence: nip
  • Translate sequence: sip
  • Translation to protein:nip
  • Translations: contig editor
  • Trev: editing the sequence
  • Trev: editing
  • Trev: fonts
  • Trev: information
  • Trev: introduction
  • Trev: opening a trace file
  • Trev: page options
  • Trev: paper options
  • Trev: pregap, use within
  • Trev: print fonts
  • Trev: print panels
  • Trev: printing a trace
  • Trev: quit
  • Trev: saving a trace file
  • Trev: scaling
  • Trev: searching
  • Trev: setting cutoffs
  • Trev: trace print bases
  • Trev: trace print colour and line width
  • Trev: trace print dash pattern
  • Trev: trace print example
  • Trev: trace print magnification
  • Trev: trace print options
  • Trev: undo
  • Trev: vector sequence
  • trev_args: pregap
  • tRNA gene search:nip
  • tRNA introns:nip
  • u

  • Unattached readings: lists
  • Uncalled base clip configuration
  • Uncalled base clip module
  • uncalled_clip.p4m
  • Undo clip edits, trev
  • Uneven positional base frequencies:nip
  • Unfinished consensus
  • Unpadded base positions
  • Update contig order
  • update_exp_file
  • update_expfile
  • use_vp_file
  • User interface: buttons
  • User interface: colour selector
  • User interface: entry boxes
  • User interface: introduction
  • User interface: menus
  • User interface: text windows
  • User interface: Zooming graphics
  • User interface
  • v

  • Variables, global to all modules
  • Variables, in modules
  • vector file formats
  • Vector sequence: screening
  • Vector_Clip: cloning site, defining
  • Vector_Clip: error codes
  • Vector_Clip: error codes
  • vector_clip: man page
  • Vector_clip: pregap, use within
  • Vector_Clip: primer site, defining
  • Vector_Clip
  • vector_file
  • Vector_primer files
  • Vectors, in Trev
  • 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_min_length: 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
  • vp_file
  • w

  • Weight matrix: splice sites:nip
  • wild type trace: trace_diff
  • Window styles
  • word_length
  • WT: wild type trace file
  • WT
  • z

  • Zoom: nip
  • Zoom: sip
  • Zooming graphics

  • home up brief full
    This document was generated using the merge_indexes.pl program.

    This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
    URL: ../manual/master_index.html