Master Table of Contents

For version-2003.0beta1

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
- 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
- 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
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
- 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

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

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_contents.html