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Master Table of Contents

For version 1.5 (2004)

For the most recent version of this documentation see the package home page.

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
- Gap4 Menus
- 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
- Consistency Display
- SNP Candidates
- Plotting Consensus Quality
  - Examining the Quality Plot
- Plotting Stop Codons
  - Examining the Plot
  - Updating the Plot
- Plotting Restriction Enzymes
Editing in Gap4
- Moving the visible segment of the contig
- Names
- Editing
- Selections
- Annotations
- Searching
- The Commands Menu
- The Settings Menu
- Removing Readings
- Primer Selection
  - Parameters
  - Template selection
- Traces
- Reference Sequence and Traces
  - Reference sequences
  - Reference traces
- Template Status Codes
- The Editor Information Line
- The Join Editor
- Using Several Editors at Once
- Quitting the Editor
- Editing Techniques
- Summary
Assembling and Adding Readings to a Database
- Normal Shotgun Assembly
- Directed Assembly
- Screen Only
- Assembly CAP2
- Assembly CAP3
- Assembly FAKII
- Assembly Phrap
- 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
- 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
- List Consensus Confidence
- List Base Confidence
Miscellaneous functions
- Complement a Contig
- Enter Tags
- Shuffle Pads
- Show Relationships
- Contig Navigation
- Sequence Search
- Extract Readings
- Automatic Clipping by Quality and Sequence Similarity
Results Manager
Lists
- Special List Names
- Basic List Commands
- Contigs To Readings Command
- Minimal Coverage Command
- Unattached Readings Command
- Highlight Readings List
- 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
- 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
- Template Status
Command Line Arguments
Converting Old Databases
- The Conversion Program
- Example
Index

Mutation Detection

Pregap4

Clipping poor data from the ends of readings

Vector clipping

Trev

Spin

The User Interface

File Formats

Manual Pages

References

Master Index

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