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Master Index

For version-2002.0

- . 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
  • .log
  • .passed
  • .phrap_log
  • .pregap4rc
  • .report
  • .scf_dir
  • .screenseq_failed
  • .screenseq_passed
  • .screenvec_failed
  • .screenvec_passed
  • .singlets
  • .svec_failed
  • .svec_passed
  • .tagrep_free
  • .tagrep_log
  • .tagrep_repeat
  • .tk_utilsrc
    •

    3

  • 3 Character Amino Acids: contig editor
    •

    _

  • _com
    •

    a

  • AC: experiment file line type
  • Active sequence: spin
  • Active tags
  • Adding modules
  • ALF/ABI to SCF conversion configuration
  • ALF/ABI to SCF conversion module
  • Align sequences: spin
  • Align: contig editor
  • aligned readings: printing
  • aligned readings: saving to file
  • aligned readings: sorted on alignment score
  • aligning pads: contig editor
  • Alignment local: spin
  • 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
  • Alt left mouse button: overview
  • alu_only
  • 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)
  • AP: experiment file line type
  • 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 problems: breaking contigs
  • assembly problems: disassembling readings
  • assembly problems: removing readings
  • 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: 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
  • Assembly
  • ATQA configuration
  • ATQA module
  • atqa.p4m
  • Augment Experiment files configuration
  • Augment Experiment files module
  • Augment, by line types
  • Augment, by text database
  • augment_exp.p4m
  • Author test:spin
  • Auto-display Traces: contig editor
  • Auto-save: contig editor
  • AV: experiment file line type
    •

    b

  • Backing up databases
  • band_width
  • Bap databases: conversion to gap4
  • Base accuracies - use of
  • Base composition plotting:spin
  • 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
  • Break contig: contig editor
  • Break contig
  • Busy file
  • BUSY files
  • 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
  • CH: experiment file line type
  • Changing the default number of matches: spin
  • Changing the maximum number of matches: spin
  • Changing the score matrix: spin
  • 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: note checks
  • Check database: reading checks
  • Check database: template checks
  • Check database: vector checks
  • Check database
  • check_params
  • Chunks, ZTR
  • circular sequences:spin
  • CL: experiment file line type
  • Clear: in output window
  • clip_mode
  • Clipping by differences
  • Clipping by quality
  • clipping readings
  • Clipping within Gap4
  • 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:spin
  • CN: experiment file line type
  • Codon composition:spin
  • Codon frequencies:spin
  • Codon tables:spin
  • Codon usage method:spin
  • Codon usage tables:spin
  • Codon usage:spin
  • Colour blindness
  • Colour configuration window
  • Colour selector
  • Colour: contig editor highlight disagreements
  • Colours
  • Command line arguments: Trev
  • Command line arguments
  • Command line arguments
  • Commands menu: contig editor
  • Comments: SCF
  • Comparator window
  • Compare Strands: contig editor
  • Complement contig
  • Complement sequence: spin
  • Component configuration
  • Components
  • Composition: sequence:spin
  • Compress Trace Files configuration
  • Compress Trace Files module
  • compress_trace.p4m
  • compression
  • Compressions: suggested experiments
  • conf_val
  • Confidence in contig editor
  • Confidence of consensus
  • Confidence values - use of
  • Confidence values graph
  • Confidence values: editing techniques
  • configuration files: pregap4
  • Configuration files
  • Configuration: pregap4 low level
  • Configure menus
  • configure: contig editor
  • Configure: restriction enzymes: spin
  • Configure: restriction enzymes
  • configure_dialogue
  • Configuring modules
  • Configuring pregap4
  • Configuring: fonts
  • Consensus algorith in contig editor
  • Consensus calculation confidence
  • Consensus calculation method
  • consensus IUB codes
  • Consensus Trace
  • Consensus: contig editor
  • Consensus: outputting
  • Conserved bases in tRNA:spin
  • Consistency display
  • Contig breaking
  • 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: 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 configuration
  • Contig Editor: saving settings
  • Contig Editor: saving to file
  • Contig Editor: saving
  • 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 menu
  • Contig Editor: trace display
  • Contig Editor: translations using feature tables
  • 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: 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 example
  • Convert program
  • convert_trace.p4m
  • convert_trace: man page
  • convert_trace
  • Copy Database
  • Copy list
  • Copy reads: dialogue
  • copy reads
  • Copy sequence: spin
  • Copy_db: man page
  • Copy_reads: 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: spin
  • CS: experiment file line type
  • Cursor dragging:spin
  • Cursor linking:spin
  • Cursor positioning:spin
  • Cursor: contig editor
  • Cursor: spin
  • Cut sites: restriction enzymes
  • Cutoff data: contig editor
  • Cutoff data: Trev
  • Cutoff values: contig editor
  • cutoff
  • Cutting sites: restriction enzymes:spin
  • CV: experiment file line type
    •

    d

  • Dap databases: conversion to bap or gap4
  • data hidden
  • Database integration
  • database limits
  • Database merging
  • database readonly access
  • Database splitting
  • Database structure: doctor database
  • database write access
  • Database, plain text format
  • 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
  • database_name
  • database_version
  • def_5_pos
  • Delete annotations
  • Delete contig: doctor database
  • Delete list
  • Delete sequence: spin
  • detection of mutations: introduction
  • diag_score
  • Difference clipping
  • difference_clip
  • Dinucleotide frequencies:spin
  • Directed assembly
  • Directories: file browser
  • directories: trace files
  • Directories
  • Disassemble readings
  • Disassembly: contig editor
  • Discrepancies: searching for in contig editor
  • Display interaction:spin
  • DNA character set
  • DNA translation:spin
  • 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
  • Doctor Database
  • Dot plot: spin
  • Dots: contig editor highlight disagreements
  • Double strand
  • Double stranded sequence listing:spin
  • DR: experiment file line type
  • Drag and drop graphics: spin
  • DT: experiment file line type
  • Dump Contig: contig editor
  • Dumping results to file:spin
  • Duplicate matches: spin
    •

    e

  • eba.p4m
  • eba: man page
  • 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
  • EMBOSS
  • EN: experiment file line type
  • enabled
  • end
  • Enter assembly configuration
  • Enter assembly module
  • enter_all
  • enter_assembly.p4m
  • entering annotations from file
  • Entering readings
  • entering tags from file
  • Entry boxes
  • Entry sequence: spin
  • 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
  • Example code
  • Example experiment file
  • Expected number of matches in spin
  • 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
  • Extension penalty for alignments
  • Extract sequence configuration
  • Extract Sequence module
  • extract_seq.p4m
  • 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
  • FASTA files: pregap4
  • Fasta output from Gap
  • Feature tables: Translation in Contig Editor
  • feature tables
  • File browser: directories
  • File browser: files
  • File browser: filters
  • File browser: formats
  • File browser: introduction
  • File browser
  • file formats for vectors
  • File menu: Contig Selector
  • File name restrictions
  • File name restrictions
  • File of filenames generation
  • File structure: SCF
  • file_error
  • file_id
  • file_type
  • Filebrowser: Trev
  • Files, specifying
  • Files: file browser
  • filtering out extraneous readings
  • Filters: file browser
  • Find best diagonals: spin
  • Find internal joins: dialogue
  • Find internal joins
  • Find matching words: spin
  • Find oligos
  • Find open reading frames:spin
  • 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 sequences
  • Find similar spans: spin
  • find_renz: man page
  • Finding genes: Introduction:spin
  • finding joins
  • finding overlaps
  • Finding protein genes:spin
  • Finding strings:spin
  • FM: experiment file line type
  • fonts, adjusting
  • Fonts, within trev
  • Fonts
  • Fonts
  • Format of protein score matrix
  • format: vector sequences
  • format: vector_primer files
  • format: vector_primer files
  • Formats: file browser
  • formats: vector files
  • Functions, builtin
  • Functions, in modules
    •

    g

  • Gap penalties for alignments
  • gap4 assembly limits
  • gap4 database limits: resetting
  • gap4 database sizes: resetting
  • gap4 database sizes
  • gap4 database: maxdb
  • gap4 database: maxseq
  • gap4 database: reading length limits
  • gap4 database: resetting sizes
  • Gap4 shotgun assembly configuration
  • Gap4 shotgun assembly module
  • gap4: resetting assembly limits
  • gap4: viewing trace files
  • Gap4
  • gap4_assemble.p4m
  • gaprc
  • Gene finding: Introduction:spin
  • General configuration configuration
  • General configuration module
  • generate_constraints
  • Genetic code:spin
  • Genetic code
  • Get sequence: spin
  • get_comment: man page
  • get_scf_field: man page
  • Global variables
  • Goto file button, trev
  • graph_d_limit
  • graph_e_limit
  • graph_o_threshold
  • Graphics rearrangement: spin
  • Graphics windows: user interface
  • Green, Phil (Phrap)
  • Group Readings by Templates: contig editor
  • GTAGDB
    •

    h

  • Header record: SCF
  • Header: SCF structure
  • Heterozygote scanner module
  • Hidden data: contig editor
  • hidden data
  • hidden data
  • Hidden data
  • hidden
  • Hide duplicate matches: spin
  • 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
  • Include config component
  • 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 sources
  • Information, in Contig Comparator
  • Information: Trev
  • init.p4m
  • init
  • init_exp.p4m
  • init_exp: man page
  • Initialise Experiment Files configuration
  • Initialise Experiment files module
  • Interaction of displays:spin
  • Interactive clipping configuration
  • Interactive clipping module
  • interactive_clip.p4m
  • Interconvert t and u: spin
  • Introduction
  • Intron in tRNA:spin
  • Intron/exon boundaries:spin
  • Invoke contig editors, in Contig Comparator
  • Invoke contig join editors, in Contig Comparator
  • Invoke template display, in Contig Comparator
  • IUB codes: consensus
  • IUB symbols:spin
    •

    j

  • Join Editor
  • joining contigs
    •

    k

  • keep_names
  • Keyboard summary (contig editor)
    •

    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
  • Line thickness configuration
  • Line types, in experiment file
  • List confidence: contig editor
  • List confidence
  • Listbox
  • 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
  • Lists
  • LN: experiment file line type
  • Load list
  • Load naming scheme
  • Load sequence: spin
  • Local alignment: spin
  • locked database
  • Long readings: suggestion of
  • low level pregap4 configuration
  • LT: experiment file line type
    •

    m

  • Magic number: SCF
  • Make_weights: man page
  • makeSCF: man page
  • mandatory
  • Marking contigs
  • marking
  • Masking contigs
  • masking
  • Match probabilities in spin
  • match_fraction
  • Matching strings:spin
  • Matrix for alignments
  • max_extent
  • max_length
  • max_pads
  • max_pmismatch
  • maxdb (command line option)
  • maxdb: gap4 assembly
  • maximum sequence length
  • maxseq (command line option)
  • maxseq: find internal joins
  • maxseq: gap4 assembly
  • maxseq
  • MC: experiment file line type
  • Memory saving: spin
  • Memory saving:spin
  • Memory usage:spin
  • Menus, configuring
  • Menus
  • Merging databases
  • Middle mouse button: overview
  • min_3_match
  • min_5_match
  • min_extent
  • min_length
  • min_match
  • minimal coverage: lists
  • minmatch
  • minscore
  • MN: experiment file line type
  • 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:spin
  • Motif searching:spin
  • motifs: spin
  • Mouse buttons: overview
  • Mouse control: overview
  • MT: experiment file line type
  • Multiple files in Trev
  • Mutation detection configuration
  • Mutation detection module
  • Mutation detection: Group Readings by Templates
  • Mutation detection: introduction
  • mutation detection: reference sequences
  • mutation detection: reference traces
  • mutation report
  • Mutation reporting: contig editor
  • Myers: Assembly (FAKII)
    •

    n

  • name
  • names in the editor
  • naming contigs
  • Naming schemes, creating.
  • naming schemes: mutation detection
  • naming schemes: pregap4
  • Naming schemes
  • NC-IUB symbols:spin
  • New database creation
  • Next button, in Contig comparator
  • Next button, trev
  • no_low_complexity
  • no_primate_rodent
  • nocheck (command line option)
  • Non-interactive processing
  • Normal consensus
  • Normalisation: codon usage tables:spin
  • Note structure: doctor database
  • Notes: editing
  • 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:spin
  • Oligo selection: contig editor
  • Oligos: choosing for probes
  • ON: experiment file line type
  • OP: experiment file line type
  • OPEN note type
  • Open penalty for alignments
  • Open reading frames:spin
  • Opening databases
  • Opening trace files: Trev
  • 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
  • PC: experiment file line type
  • PD: primer data - the sequence of a primer
  • Percentage matches:spin
  • Persistence of results:spin
  • Personal search: spin
  • Phrap assembly configuration
  • Phrap assembly module
  • Phrap Assembly
  • phrap_assemble.p4m
  • Phred configuration
  • Phred module
  • phred.log
  • phred.p4m
  • plain text
  • Plot stop codons: examining the plot
  • Plot stop codons: updating the plot
  • Plot stop codons
  • Plotting base composition:spin
  • PN: experiment file line type
  • polyA clipping
  • polyA_clip: man page
  • polyT clipping
  • PR: experiment file line type
  • pregap4.config
  • pregap4: FASTA files
  • pregap4: naming schemes
  • pregap4: Reference sequence
  • pregap4: temporary files
  • Pregap4
  • pregap4rc files
  • pregap4rc
  • Previous button, trev
  • Primer Selection: contig editor
  • Primer selection: contig editor
  • Primer site, defining
  • Primer site, finding
  • Primers: suggestion of
  • Print list
  • Printing contigs
  • printing: aligned readings
  • Private data: SCF
  • Probabilities in spin
  • probability
  • process_dialogue
  • protein alignment symbols: spin
  • Protein score matrix format
  • Protein:spin
  • PS: experiment file line type
    •

    q

  • Qclip: man page
  • QL: experiment file line type
  • QR: experiment file line type
  • Quality calculation algorithm
  • quality clip configuration
  • Quality clip module
  • Quality clipping
  • Quality codes
  • Quality in contig editor
  • Quality plot: examining the plot
  • Quality plot: template display
  • Quality plot
  • Quality values - use of
  • Quality values: contig editor, displayed
  • Quality values: contig editor, use within
  • Quality: output for consensus
  • quality_clip.p4m
  • quality_clip
  • Quit: Trev
  • Quitting: contig editor
    •

    r

  • Range: spin
  • RAWD note type
  • RAWDATA
  • Read pair data and contig ordering
  • Read pairs
  • read raid
  • Read sequence: spin
  • Read-pair coverage
  • READ_BRIEF_FORMAT
  • read_only (command line option)
  • reading clipping
  • Reading coverage
  • Reading frame:spin
  • reading length limits in gap4
  • Reading name length restrictions
  • Reading name restrictions
  • Reading name restrictions
  • reading names in the editor
  • Reading names, searching for
  • Reading names
  • Reading numbers
  • reading percent mismatch
  • Reading plot: template display
  • Reading structure: doctor database
  • Readings list: template display
  • readings list
  • readings: copying to other databases
  • readings: entering
  • readings: extraneous
  • Readings: maximum in a database
  • readings: sorted on alignment score
  • readonly database
  • readonly
  • reads: copying to other databases
  • Records in experiment files
  • Redirect output
  • Reference sequence: contig editor
  • Reference sequence: pregap4
  • reference sequences
  • Reference trace module
  • Reference traces: contig editor
  • reference traces
  • references
  • Reject button, trev
  • Remove reading: contig editor
  • Remove, in Contig Comparator
  • removing extraneous readings
  • Removing modules
  • Removing readings
  • Removing results
  • Repeat search
  • repeat_file
  • repeat_masker.p4m
  • RepeatMasker configuration
  • RepeatMasker module
  • repeats_masker.p4m
  • Report mutations: contig editor
  • report
  • Restriction enzyme files
  • Restriction enzyme sites:spin
  • Restriction enzymes: configuring: spin
  • Restriction enzymes: configuring
  • Restriction enzymes: cut sites
  • Restriction enzymes: examining the plot: spin
  • Restriction enzymes: examining the plot
  • Restriction enzymes: introduction: spin
  • Restriction enzymes: selecting enzymes: spin
  • Restriction enzymes: selecting enzymes
  • Restriction enzymes: tags, creation of
  • Restriction enzymes: template display
  • Restriction enzymes: textual output
  • Restriction enzymes
  • Restriction site listing:spin
  • Restriction site printing:spin
  • 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: spin
  • Results manager
  • Results menu: Contig Selector
  • Results: removing
  • Right mouse button: overview
  • right_num_uncalled
  • right_win_length
  • Rotate sequence: spin
  • RS: experiment file line type
  • 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: spin
  • saving contigs to file
  • Saving: contig editor
  • Saving: Trev
  • SC: experiment file line type
  • SC
  • 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
  • Score matrix format
  • score
  • Scramble sequence: spin
  • Screen for unclipped vector configuration
  • Screen for unclipped vector module
  • Screen only: assembly
  • Screen sequences configuration
  • Screen sequences module
  • 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_vector.p4m
  • Screening against vector sequence
  • screening for bacterial sequences
  • screening for vectors
  • Screening readings for contaminant sequences
  • Scroll on output
  • SE: experiment file line type
  • Search annotation contents: lists
  • Search sequence names: lists
  • Search template names: lists
  • 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 for motifs:spin
  • Searching for oligos:spin
  • Searching for strings:spin
  • Searching reading name: contig editor
  • Searching: contig editor
  • Searching: motifs:spin
  • Searching: open reading frames:spin
  • Searching: protein genes:spin
  • Searching: splice sites:spin
  • Searching: start codons:spin
  • Searching: stop codons:spin
  • Searching: Trev
  • Searching: tRNA genes:spin
  • Searching:spin
  • security
  • Select tags: template display
  • Selecting a sequence: spin
  • selecting contigs: Contig Selector
  • Selections: contig editor
  • Seq identifier: spin
  • Sequence composition:spin
  • Sequence display: spin
  • Sequence display:spin
  • Sequence interpretation: finding protein genes:spin
  • Sequence interpretation: tRNA gene search:spin
  • sequence length, maximum
  • Sequence manager: spin
  • Sequence names, searching for
  • Sequence scrolling:spin
  • Sequence Search
  • Sequence viewer:spin
  • 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 genetic code:spin
  • Set genetic code
  • Set or unset saving of undo: contig editor
  • Set Output List: contig editor
  • Set the range: spin
  • Settings menu: contig editor
  • Settings: saving in contig editor
  • SF: experiment file line type
  • SF
  • 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
  • Shutdown configuration
  • shutdown.p4m
  • shutdown
  • SI: experiment file line type
  • Significance of matches in spin
  • Sim: spin
  • Simple search: spin
  • Simple Text Database
  • simple_only
  • simultaneous database access
  • Single stranded regions: assembling into
  • Single stranded sequence listing:spin
  • Sites: restriction enzymes:spin
  • SL: experiment file line type
  • Smith-Waterman: spin
  • Sort Matches
  • SP: experiment file line type
  • SP
  • SPIN Sequence Comparison Plot: spin
  • SPIN Sequence Plot: spin
  • Spin: copy sequence
  • Spin: sequence type (linear or circular)
  • Spin
  • Splice junctions:spin
  • Splice sites:spin
  • Splitting databases
  • SQ: experiment file line type
  • SR: experiment file line type
  • SS: experiment file line type
  • ST: experiment file line type
  • Start codons:spin
  • start
  • Status line: contig editor
  • Stems and loops:spin
  • Stop codons display
  • Stop codons: examining the plot
  • Stop codons: updating the plot
  • Stop codons:spin
  • Stops: suggested experiments
  • strand coverage
  • String finding:spin
  • String matching:spin
  • string search
  • String searching:spin
  • Styles of windows
  • Subsequence searching:spin
  • 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
    •

    t

  • Tag database
  • Tag repeats configuration
  • Tag repeats module
  • Tag Selector
  • TAG_BRIEF_FORMAT
  • tag_repeats.p4m
  • tag_type
  • tag_types
  • Tags, searching for
  • Tags: contig editor
  • tags: entering from a file
  • 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: 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 names, searching for
  • Template plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Templates: grouping readings in contig editor
  • temporary files
  • Text windows
  • TG: experiment file line type
  • Tips on assembly
  • tk_utilsrc
  • TN: experiment file line type
  • to_scf.p4m
  • Toggle auto-save: contig editor
  • Trace difference module
  • Trace differences: contig editor
  • Trace Display menu: contig editor
  • Trace displays: contig editor
  • Trace file location
  • trace files: defining location
  • trace files: location
  • Trace Format Conversion configuration
  • Trace Format Conversion
  • Trace: Consensus Trace
  • trace_diff.p4m
  • tracediff: man page
  • Transcribe sequence: spin
  • Translate sequence: spin
  • Translation to protein:spin
  • Translations: contig editor
  • Trev: editing the sequence
  • Trev: editing
  • Trev: fonts
  • Trev: information
  • Trev: introduction
  • Trev: opening trace files
  • Trev: page options
  • Trev: paper options
  • 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: trace print title
  • Trev: undo
  • Trev: vector sequence
  • Trev
  • tRNA gene search:spin
  • tRNA introns:spin
    •

    u

  • Unattached readings: lists
  • Uncalled base clip configuration
  • uncalled_clip.p4m
  • Undo clip edits, trev
  • Undo toggle: contig editor
  • Undo: contig editor
  • Uneven positional base frequencies:spin
  • Unfinished consensus
  • Unpadded base positions
  • Unpadded positions in editor
  • Update contig order
  • update_exp_file
  • update_expfile
  • use_sample_name
  • 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
  • User levels
    •

    v

  • Variables, global to all modules
  • Variables, in modules
  • vector file formats
  • Vector sequence: screening
  • vector sequences format
  • Vector_Clip: cloning site, defining
  • Vector_Clip: error codes
  • Vector_Clip: error codes
  • vector_clip: man page
  • Vector_Clip: primer site, defining
  • Vector_Clip
  • vector_file
  • vector_list
  • Vector_Primer files
  • Vector_primer files
  • Vectors, in Trev
  • Verfiy AND: contig editor
  • Verfiy OR: contig editor
  • View menu: Contig Selector
  • vp_file
  • vp_length
    •

    w

  • Weight matrix: splice sites:spin
  • Weight matrix:spin
  • Window styles
  • window_length
  • word_length
  • WT: wild type trace file
  • WT
    •

    z

  • Zoom: spin
  • Zooming graphics
  • ZTR Chunk format
  • ZTR Chunk types
  • ZTR header
  • ZTR References
  • ZTR Text Identifiers
  • ZTR
    •
    home up brief full
    This document was generated using the merge_indexes.pl program.

    This page is maintained by staden-package. Last generated on 22 October 2002.
    URL: ../manual/master_unix_index.html