The Staden Package Mini-Manual

• Preface
• Sequence Assembly and Finishing Using Gap4
• 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
• Searching for point mutations using pregap4 and gap4
  • Introduction to mutation detection
    • Mutation Detection Programs
    • Mutation Detection Reference Data
    • Reference Sequences
    • Reference Traces
    • Using The Template Display With Mutation Data
    • Configuring The Gap4 Editor For Mutation Data
    • Using The Gap4 Editor With Mutation Data
    • Processing Batches Of Mutation Data Trace Files
    • Processing Batches Of Mutation Data Trace Files Using Pregap4
    • Configuration Of Pregap4 For Mutation Data
    • Discussion Of Mutation Data Processing Methods
• Preparing Readings for Assembly Using Pregap4
• Introduction
  • Summary of the Files used and the Processing Steps
  • Introduction to the Pregap4 User Interface
    • Introduction to the Files to Process Window
    • Introduction to the Configure Modules Window
    • Introduction to the Textual Output Window
    • Introduction to Running Pregap4
• Viewing Traces Using Trev
• Analysing Sequences Using Spin
• Introduction
  • Summary of the Spin Single Sequence Functions
  • Summary of the Spin Comparison Functions
  • Introduction to the Spin User Interface
    • Introduction to the Spin Plot
    • Introduction to the Spin Sequence Display
    • Introduction to the Spin Sequence Comparison Plot
    • Introduction to the Spin Sequence Comparison Display

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