CSC

	Tehdyt toimenpiteet Master Index For version-2003.0beta1 - . 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 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 naming scheme Mutation detection: Group Readings by Templates Mutation detection: introduction mutation detection: reference sequences mutation detection: reference traces mutation report Mutation reporting: contig editor Mutation scanner module mutation_detection.p4t 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 This document was generated using the merge_indexes.pl program. This page is maintained by staden-package. Last generated on 25 April 2003. URL: ../manual/master_unix_index.html