Gap4

• Organisation of the gap4 Manual
• Introduction
  • Summary of the Files used and the Preprocessing Steps
  • Summary of Gap4's Functions
  • Introduction to the gap4 User Interface
    • Introduction to the Contig Selector
    • Introduction to the Contig Comparator
    • Introduction to the Template Display
    • Introduction to the Consistency Display
    • Introduction to the Restriction Enzyme Map
    • Introduction to the Stop Codon Map
    • Introduction to the Contig Editor
    • Introduction to the Contig Joining Editor
  • Gap4 Menus
    • Gap4 File menu
    • Gap4 Edit menu
    • Gap4 View menu
    • Gap4 Options menu
    • Gap4 Experiments menu
    • Gap4 Lists menu
    • Gap4 Assembly menu
  • The use of numerical estimates of base calling accuracy
  • Use of the "hidden" poor quality data
  • Annotating and masking readings and contigs
    • Standard tag types
    • Active tags and masking
• Contig Selector
  • Selecting Contigs
  • Changing the Contig Order
  • The Contig Selector Menus
• Contig Comparator
  • Examining Results and Using Them to Select Commands
  • Automatic Match Navigation
• Contig Overviews
  • Template Display
    • Reading and Template Plot
      • Reading and Template Plot Display
      • Reading and Template Plot Options
      • Reading and Template Plot Operations
    • Quality Plot
    • Restriction Enzyme Plot
  • Consistency Display
    • Confidence Values Graph
    • Reading Coverage Histogram
    • Read-Pair Coverage Histogram
    • Strand Coverage
  • Plotting Consensus Quality
    • Examining the Quality Plot
  • Plotting Stop Codons
    • Examining the Plot
    • Updating the Plot
  • Plotting Restriction Enzymes
    • Selecting Enzymes
    • Examining the Plot
    • Reconfiguring the Plot
    • Creating Tags for Cut Sites
    • Textual Outputs
• Editing in Gap4
  • Moving the visible segment of the contig
  • Names
  • Editing
    • Moving the editing cursor
    • Editing Modes
    • Adjusting the Quality Values
    • Adjusting the Cutoff Data
    • Summary of Editing Commands
  • Selections
  • Annotations
  • Searching
    • Search by Position
    • Search by Problem
    • Search by Annotation Comments
    • Search by Tag Type
    • Search by Sequence
    • Search by Quality
    • Search by Consensus Quality
    • Search by file
    • Search by Reading Name
    • Search by Edit
    • Search by Evidence for Edit (1)
    • Search by Evidence for Edit (2)
    • Search by Discrepancies
  • The Commands Menu
    • Search
    • Create Tag
    • Edit Tag
    • Delete Tag
    • Save Contig
    • Dump Contig to File
    • Save Consensus Trace
    • List Confidence
    • Report Mutations
    • Select Primer
    • Align
    • Shuffle Pads
    • Remove Reading
    • Break Contig
  • The Settings Menu
    • Status Line
    • Trace Display
    • Consensus Algorithm
    • Highlight Disagreements
    • Compare Strands
    • Toggle auto-save
    • 3 Character Amino Acids
    • Group Readings by Templates
    • Show Reading and Consensus Quality
    • Show edits
    • Show Unpadded Positions
    • Set Active Tags
    • Set Output List
    • Set Default Confidences
    • Set or unset saving of undo
  • Removing Readings
  • Primer Selection
    • Parameters
    • Template selection
  • Traces
  • Reference Sequence and Traces
    • Reference sequences
    • Reference traces
  • The Editor Information Line
    • Reading Information
    • Contig Information
    • Tag Information
    • Base Information
  • The Join Editor
  • Using Several Editors at Once
  • Quitting the Editor
  • Editing Techniques
    • Consensus and Quality Cutoffs
    • Editing by Base Change or Confidence
    • Base Overcalls
    • Base Undercalls
    • Multiple Base Disagreements
    • Poor Quality
    • Checking for Errors
  • Summary
    • Keyboard summary for editing window
    • Mouse summary for editing window
    • Mouse summary for names window
    • Mouse summary for scrollbar
• Assembling and Adding Readings to a Database
  • Normal Shotgun Assembly
    • Assemble Independently
    • Assemble Into Single Stranded Regions
    • Stack Readings
    • Put All Readings In Separate Contigs
  • Directed Assembly
  • Screen Only
  • Assembly CAP2
    • Perform CAP2 assembly
    • Import CAP2 assembly
    • Perform and import CAP2 assembly
    • Stand alone CAP2 assembly
  • Assembly CAP3
    • Perform CAP3 assembly
    • Import CAP3 assembly
    • Perform and import CAP3 assembly
    • Stand alone CAP3 assembly
    • Further details about CAP3
  • Assembly FAKII
    • Perform FAKII assembly
    • Import FAKII assembly
    • Perform and import FAKII assembly
  • Assembly Phrap
    • Before Using Phrap
    • Phrap Assembly
    • Phrap Reassembly
    • Phrap on the Command Line
  • General Comments and Tips on Assembly
  • Assembly Failure Codes
• Ordering and Joining Contigs
  • Order contigs
  • Find Read Pairs
    • Find Read Pairs Graphical Output
    • Find Read Pairs Text Output
      • The Template Lines
      • The Reading Lines
  • Find Internal Joins
    • Find Internal Joins Dialogue
  • Find Repeats
• Checking Assemblies and Removing Readings
  • Checking Assemblies
  • Removing Readings and Breaking Contigs
    • Breaking Contigs
    • Disassembling Readings
• Finishing Experiments
  • Double Stranding
  • Suggest Primers
  • Suggest Long Readings
  • Compressions and Stops
  • Suggest Probes
• Calculating Consensus Sequences
  • Normal Consensus Output
  • Extended Consensus Output
  • Unfinished Consensus Output
  • Quality Consensus Output
  • The Consensus Algorithms
    • Consensus Calculation Using Base Frequencies
    • Consensus Calculation Using Weighted Base Frequencies
    • Consensus Calculation Using Confidence values
    • The Quality Calculation
  • List Consensus Confidence
• Miscellaneous functions
  • Complement a Contig
  • Enter Tags
  • Show Relationships
  • Sequence Search
  • Extract Readings
  • Automatic Clipping by Quality and Sequence Similarity
    • Difference Clipping
    • Quality Clipping
• Results Manager
• Lists
  • Special List Names
  • Basic List Commands
  • Contigs To Readings Command
  • Minimal Coverage Command
  • Unattached Readings Command
  • Search Sequence Names
  • Search Template Names
  • Search Annotation Contents
• Notes
  • Selecting Notes
  • Editing Notes
  • Special Note Types
• Gap4 Database Files
  • Directories
  • Opening a New Database
  • Opening an Existing Database
  • Making Backups of Databases
  • Reading and Contig Names and Numbers
• Copy Readings
  • Introduction
    • Copy Reads Dialogue
• Check Database
  • Database Checks
  • Contig Checks
  • Reading Checks
  • Annotation Checks
  • Note Checks
  • Template Checks
  • Vector Checks
  • Clone Checks
• Doctor Database
  • Structures Menu
    • Database Structure
    • Reading Structure
    • Contig Structure
    • Annotation Structure
    • Template Structure
    • Original Clone Structure
    • Note Structure
  • Ignoring Check Database
  • Extending Structures
  • Listing and Removing Annotations
  • Shift Readings
  • Delete Contig
  • Reset Contig Order
• Configuring
  • Introduction
  • Consensus Algorithm
  • Set Maxseq/Maxdb
  • Set Fonts
  • Colour Configuration Window
  • Configuring Menus
  • Set Genetic Code
  • Alignment Scores
  • Trace File Location
  • The Tag Selector
  • The GTAGDB File
• Command Line Arguments
• Converting Old Databases
  • The Conversion Program
  • Example
• Index

This document was generated on 25 April 2003 using the texi2html translator version 1.39 (with local modifications)