Master Table of Contents

For version-1996.1

File Formats

• Introduction
• SCF
  • Header Record
  • Sample Points.
  • Sequence Information.
  • Comments.
  • Private data.
  • File structure.
  • Notes
    • Byte ordering and integer representation.
• Experiment File
  • Records
  • Explanation of Records
  • Example
  • Unsupported Additions (From LaDeana Hillier)
• Restriction Enzyme File
• Index

Pregap

• Introduction
• The Processes Performed
• User Interaction
• Automation -- the .pregaprc file
• Further Pregap Configuration
• Integration with External Databases
  • Example Integration - Simple Database
  • Example Integration - Full Database
  • Example Integration - Squirrel Database
• Final Notes
• Summary of Variables Used
• The Internals of the Pregap Script
• Index

Vepe and Repe

• Screening Against Vector Sequences and Restriction Enzymes
  • Introduction
  • Defining the Positions of Cloning and Primer Sites for Vepe
    • The positions of SmaI site and a forward and reverse primer for M13MP18
  • Finding the Cloning Site
  • Finding the Primer Site
    • The Forward Primer
    • The Reverse Primer
  • How to do the calculations in a Single Step
    • The Forward Primer
    • The Reverse Primer
  • Screening for Restriction Sites
• Screening Readings for Repeat Families
  • Using Repe for Other Sequence Families
• Index

The User Interface

• Introduction
• Basic Interface Controls
  • Buttons
  • Menus
  • Text Windows
  • Text Entry Boxes
• Standard Mouse Operations
• The Output and Error Windows
• Graphics Window
  • Introduction
  • Zooming
• Colour Selector
• Tag Selector
• File Browser
• Introduction
  • Directories and Files
  • Filters
• Index

Trev

• Introduction
• Opening a trace file
  • Opening a trace file from the command line
  • Opening a trace file from within Trev
• Viewing the trace
  • Searching
  • Information
• Editing
  • Setting the left and right cutoffs
  • Editing the sequence
• Saving a trace file
• Quitting
• Index

Gap version 4

• Introduction
  • Command Line Arguments
  • The use of numerical estimates of base calling accuracy
    • Checking and editing contigs the old way
    • Basis of the new method of editing
    • Checking and editing contigs the new way
    • Consequences of the new editing strategy
    • Current status of the new editing strategy
  • Annotating and masking readings and contigs
    • Standard tag types
    • Active tags and masking
  • Use of the 'hidden' poor quality data
• Gap Database Files
  • Introduction
  • Opening a New Database
  • Opening an Existing Database
  • Making Backups of Databases
  • Reading and Contig Names and Numbers
• Converting Old Databases
  • Introduction
  • The Conversion Program
  • Example
• Configuring
  • Introduction
  • Options Menu
  • Colour Configuration Window
  • The .gaprc file
  • The GTAGDB File
• Check Database
  • Introduction
  • Database Checks
  • Contig Checks
  • Reading Checks
  • Annotation Checks
  • Template Checks
  • Vector Checks
  • Clone Checks
• Entering Readings into the Database (Assembly)
  • Normal Shotgun Assembly
  • Assemble Independently
  • Assemble Into Single Stranded Regions
  • Put All Readings In One Contig
  • Put All Readings In New Contigs
  • Directed Assembly
  • Enter Pre-assembled data
  • Screen Only
  • Tips
  • Assembly Failure Codes
• Contig Selector
  • Introduction
  • Selecting Contigs
  • Changing the Contig Order
  • View Menu
• Contig Comparator
  • Introduction
  • Examining Results and Using Them to Select Commands
• Results Manager
• Editing in Gap4
  • Introduction
  • Movement
  • Names
  • Editing
    • Editing Modes
    • Insertion and Deletion of Bases
    • Shifting Readings
    • Pads
    • 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 Sequence
    • Search by Quality
    • Search by Reading Name
    • Search by Edit
    • Search by Verify AND
    • Search by Verify OR
    • Search by Tag Type
  • The Commands Menu
    • Search
    • Create Tag
    • Edit Tag
    • Delete Tag
    • Save Contig
    • Dump Contig to File
    • Select Primer
    • Align
    • Shuffle Pads
  • The Settings Menu
    • Status Line
    • Highlight Disagreements
    • Compare Strands
    • Auto-display Traces
    • Toggle auto-save
    • 3 Character Amino Acids
    • Show Quality
    • Set Active Tags
    • Set Output List
  • Primer Selection
    • Parameters
    • Template selection
  • Traces
  • The Join Editor
  • Using Several Editors at Once
  • Quitting the Editor
  • Summary
    • Key summary for editing window
    • Mouse summary for editing window
    • Mouse summary for names window
    • Mouse summary for scrollbar
• Template Display
  • Introduction
  • Reading and Template Plot
  • Active Readings
  • Quality Plot
  • Restriction Enzyme Plot
  • Tags
• Plotting Stop Codons
  • Introduction
  • Examining the Plot
  • Updating the Plot
• Plotting Restriction Enzymes
  • Introduction
  • Selecting Enzymes
  • Examining the Plot
  • Reconfiguring the Plot
  • Creating Tags for Cut Sites
• Find Internal Joins
  • Introduction
  • Dialogue
• Find Repeats
• Find Read Pairs
  • Introduction
  • Display
  • Output
    • The Template Lines
    • The Reading Lines
• Check Assembly
• Find Oligos
• Break Contig
• Disassemble Readings
• Double Stranding
• Suggest Primers
• Suggest Long Readings
• Compressions and Stops
• Suggest Probes
• Complement a Contig
• Enter Tags
• Calculate Consensus
  • Introduction
  • Normal
  • Extended
  • Unfinished
  • Quality
  • The Consensus Calculation
    • The Quality Calculation
• Extract Readings
• Show Relationships
• Lists
  • Introduction
  • Basic List Commands
  • Minimal Coverage Command
  • Unattached Readings Command
• Doctor Database
  • Introduction
  • Structures Menu
    • Database Structure
    • Reading Structure
    • Contig Structure
    • Annotation Structure
    • Template Structure
    • Original Clone Structure
    • Vector Structure
  • Extending Structures
  • Listing and Removing Annotations
  • Shift Readings
  • Delete Contig
  • Reset Contig Order
• Index

Manual Pages

• Clip
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • SEE ALSO
• Eba
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • EXAMPLES
  • SEE ALSO
• Get_scf_field
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • SEE ALSO
• Init_exp
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • NOTES
  • SEE ALSO
• MakeSCF
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • EXAMPLES
  • NOTES
  • SEE ALSO
• Extract_seq
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • SEE ALSO
• Trace_clip
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • SEE ALSO
• Scale_trace_clip
  • NAME
  • SYNOPSIS
  • DESCRIPTION
  • OPTIONS
  • SEE ALSO
• Index

Sip

• Introduction
• Reading in sequences
  • Extract a sequence from a sequence library
  • Extract a sequence from a personal file
• Sequence manager
  • Change the active sequence
  • Complement sequence
  • Translate sequence
  • Scramble sequence
  • Save sequence
  • Delete sequence
• Result manager
• Permanent and temporary results
• Find similar spans
• Find matching words
• Find best diagonals
• Align sequences
• Sip plot
  • Redisplaying temporary results
  • Crosshairs
  • Zoom
• Sequence display
• Changing the score matrix
• Changing the maximum number of matches
• Changing the default number of matches
• Probabilities and expected numbers of matches
• Index

Sequence Library Browser

• Introduction
• Performing the search
  • Library selection
  • Field selection
  • Entering the search word
  • Search mode
• Results of the search
• Operations on the Results
• Listing entrynames
• Combining results
• Deleting results or entrynames
• Selecting the output parameters
• Listing the contents of a result or entry
• Interface with parent program
• Maximum number of entries
• Index

Master Index

This page is maintained by James Bonfield. Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/master_contents.html