Master Table of Contents
For version 1.5 (2004)
For the most recent version of this documentation see the package
home page
.
Gap4
Copyright
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
2nd-Highest Confidence
Diploid Graph
SNP Candidates
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
Search by Consensus 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
Remove Reading
Break Contig
The Settings Menu
Status Line
Trace Display
Auto-display Traces
Show Read-pair Traces
Auto-diff Traces
Y scale differences
Consensus Algorithm
Group Readings
Highlight Disagreements
Compare Strands
Toggle auto-save
3 Character Amino Acids
Show Reading and Consensus Quality
Show edits
Show Unpadded Positions
Show Template Names
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
Template Status Codes
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
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
Difference Clipping
Quality Clipping
Quality Clip Ends
N-Base Clipping
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
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
Template Status
Command Line Arguments
Converting Old Databases
The Conversion Program
Example
Index
Gap5
Copyright
Gap5 Databases
Creating databases
Opening/closing databases
Changing directories
Check Database
Contig Selector / Comparator
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
Template Display
Filtering data
Template plot
Controlling The Y Layout.
Depth / Coverage Plot
Editing in Gap5
Moving the visible segment of the contig
Names
Editing
Moving the editing cursor
Adjusting the Quality Values
Adjusting the alignment coordinates
Adjusting the Cutoff Data
Summary of Editing Commands
Cut and Paste Control of Sequence
Selecting Sequences
Annotations
Annotation Macros
Searching
Search by Annotation Comments
Search by Tag Type
Search by Padded Position
Search by Unpadded Position
Search by Sequence
Search by Reading Name
Search by Reference InDel
Search by Consensus Quality
Search by Consensus Discrepancy
Search by Consensus Heterozygosity
Search by Low Coverage
Search by High Coverage
The Settings Menu
Group Readings
Highlight Disagreements
Pack Sequences
Hide Annotations
Primer Selection
Traces
The Editor Information Line
Reading Information
Contig Information
Tag Information
The Join Editor
Using Several Editors at Once
Quitting the Editor
Summary
Keyboard summary for editing window
Mouse summary for editing window
Mouse summary for names window
Plotting Restriction Enzymes
Selecting Enzymes
Examining the Plot
Reconfiguring the Plot
Textual Outputs
Importing and Exporting Data
Assembly
Importing with tg_index
Importing fasta/fastq files
Mapped assembly by bwa aln
Mapped assembly by bwa dbwtsw
Importing GFF
Export Tags
Export Sequences
Finding Sequence Matches
Find Internal Joins
Find Internal Joins Dialogue
Find Repeats
Find Read Pairs
Find Read Pairs Graphical Output
Sequence Search
Checking Assemblies and Removing Readings
Checking Assemblies
Removing Readings and Breaking Contigs
Breaking Contigs
Disassembling Readings
Delete Contigs
Tidying up alignments
Shuffle Pads
Remove Pad Columns
Remove Contig Holes
Calculating Consensus Sequences
Normal 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
List Base Confidence
Other Miscellany
List Libraries
Results Manager
Lists
Special List Names
Basic List Commands
Contigs To Readings Command
Search Sequence Names
Index
Mutation Detection
Copyright
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
Index
Pregap4
Copyright
Organisation of the Pregap4 Manual
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
Pregap4 Menus
Pregap4 File menu
Pregap4 Modules menu
Pregap4 Information source menu
Pregap4 Options menu
Specifying Files to Process
Running Pregap4
Non Interactive Processing
Command Line Arguments
Configuring the Pregap4 User Interface
Fonts and Colours
Window Styles
Configuring Modules
General Configuration
Estimate Base Accuracies
Phred
ATQA
Trace Format Conversion
Compress Trace Files
Initialise Experiment Files
Augment Experiment Files
Quality Clip
Sequencing Vector Clip
Cross_match
Cloning Vector Clip
Screen for Unclipped Vector
Screen Sequences
Blast Screen
Interactive Clipping
Extract Sequence
RepeatMasker
Tag Repeats
Mutation Detection
Reference Traces and Reference Sequences
Trace Difference
Mutation Scanner
Gap4 Shotgun Assembly
Cap2 Assembly
Cap3 Assembly
FakII Assembly
Phrap Assembly
Enter Assembly into Gap4
Email
Old Cloning Vector Clip - Obsolete
ALF/ABI to SCF Conversion - Obsolete
Using Config Files
Pregap4 Naming Schemes
Mutation Detection Naming Scheme
Old Sanger Centre Naming Scheme
New Sanger Centre Naming Scheme
Writing Your Own Naming Schemes
Pregap4 Components
Information Sources
Simple Text Database
Experiment File Line Types
Adding and Removing Modules
Low Level Pregap4 Configuration
Low Level Global Configuration
Low Level Component Configuration
Low Level Module Configuration
General Configuration
ALF/ABI to SCF Conversion
Estimate Base Accuracies
Phred
ATQA
Compress Trace Files
Trace Format Conversion
Initialise Experiment Files
Augment Experiment Files
Uncalled Base Clip
Quality Clip
Sequencing Vector Clip
Cross_match
Cloning Vector Clip
Old Cloning Vector Clip
Screen for Unclipped Vector
Screen Sequences
Blast Screen
Interactive Clipping
Extract Sequence
Tag Repeats
RepeatMasker
Mutation Detection
Gap4 Shotgun Assembly
Cap2 Assembly
Cap3 Assembly
FakII Assembly
Phrap Assembly
Enter Assembly into Gap4
Email
Shutdown
Writing New Modules
An Overview of a Module
Functions
Module Variables
Global Variables
Builtin Functions
An Example Module
General Index
File Index
Variable Index
Function Index
Clipping poor data from the ends of readings
Copyright
Introduction to read clipping
Index
Vector clipping
Copyright
Screening Against Vector Sequences
Introduction
Algorithms
Options
Parameters (defaults in brackets)
Error codes
Examples
Vector_Primer file format
Vector_Primer File Notes
Defining Cloning and Primer Sites for Vector_Clip
Finding the Cloning and Primer Sites
Screening Readings for Contaminant Sequences
Introduction
Parameters
Limits
Error codes
Examples
Index
Trev
Copyright
Introduction
Opening trace files
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
Undoing clip edits
Saving a trace file
Processing multiple files
Printing a trace
Page options
Paper options
Panels
Fonts
Trace options
Title
Line width and colour
Dash pattern
Print bases
Print magnification
Example
Quitting
Index
Spin
Copyright
Organisation of the Spin Manual
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
Spin Menus
Spin File Menu
Spin View Menu
Spin Options Menu
Spin Sequences Menu
Spin Statistics Menu
Spin Translation Menu
Spin Search Menu
Spin Comparison Menu
Spin Emboss Menu
Spin's Analytical Functions
Count Sequence Composition
Count Dinucleotide Frequencies
Plot base composition
Calculate codon usage
Set genetic code
Translation - general
Find open reading frames
Restriction enzyme search
Selecting Enzymes
Examining the Plot
Reconfiguring the Plot
Printing the sites
Subsequence search
Motif search
Gene finding
Start codon search
Stop codon search
Codon usage method
Positional base preferences
Author test
Uneven positional base preferences
Splice site search
tRNA search
Spin Comparison Functions
Finding Similar Spans
Finding Matching Words
Finding the Best Diagonals
Aligning Sequences Globally
Aligning Sequences Locally
Controlling and Managing Results
Probabilities and expected numbers of matches
Changing the maximum number of matches
Changing the default number of matches
Hide duplicate matches
Changing the score matrix
Set protein alignment symbols
The Spin User Interface
SPIN Sequence Plot
Cursors
Crosshairs
Zoom
Drag and drop
Sequence display
Search
Save
SPIN Sequence Comparison Plot
Cursors
Crosshairs
Zoom
Drag and drop
Sequence Comparison Display
Controlling and Managing Results
Result manager
Information
List
Configure
Hide
Reveal
Remove
Reading and Managing Sequences
Use of feature tables in spin
Reading in sequences
Simple search
Extracting a sequence from a personal archive file
Sequence manager
Change the active sequence
Set the range
Copy Sequence
Sequence type
Complement sequence
Interconvert t and u
Translate sequence
Scramble sequence
Rotate sequence
Save sequence
Delete sequence
Selecting a sequence
Index
The User Interface
Copyright
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
File Browser
Introduction
Directories and Files
Filters
Font Selection
Index
File Formats
Copyright
Introduction
SCF
Header Record
Sample Points.
Sequence Information.
Comments.
Private data.
File structure.
Notes
Byte ordering and integer representation.
Compression of SCF Files
ZTR
Header
Chunk Format
Data format 0 - Raw
Data format 1 - Run Length Encoding
Data format 2 - ZLIB
Data format 64/0x40 - 8-bit delta
Data format 65/0x41 - 16-bit delta
Data format 66/0x42 - 32-bit delta
Data format 67-69/0x43-0x45 - reserved
Data format 70/0x46 - 16 to 8 bit conversion
Data format 71/0x47 - 32 to 8 bit conversion
Data format 72/0x48 - "follow" predictor
Data format 73/0x49 - floating point 16-bit chebyshev polynomial predictor
Data format 74/0x4A - integer based 16-bit chebyshev polynomial predictor
Chunk Types
SAMP
SMP4
BASE
BPOS
CNF4
TEXT
CLIP
CR32
COMM
Text Identifiers
References
Experiment File
Records
Explanation of Records
Example
Unsupported Additions (From LaDeana Hillier)
Restriction Enzyme File
Vector_primer File
Vector Sequence Format
Index
Manual Pages
Copyright
Convert_trace
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
NOTES
SEE ALSO
Copy_db
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
NOTES
Copy_reads
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLE
Eba
NAME
SYNOPSIS
DESCRIPTION
EXAMPLES
SEE ALSO
Extract_seq
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Extract_fastq
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Find_renz
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
GetABIfield
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
SEE ALSO
Get_comment
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Get_scf_field
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Hash_exp
NAME
SYNOPSIS
DESCRIPTION
SEE ALSO
Hash_extract
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Hash_list
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
Hash_tar
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
SEE ALSO
Init_exp
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
NOTES
SEE ALSO
MakeSCF
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
NOTES
SEE ALSO
Make_weights
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLE
SEE ALSO
PolyA_clip
NAME
SYNOPSIS
OPTIONS
DESCRIPTION
SEE ALSO
Qclip
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLE
SEE ALSO
Screen_seq
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
NOTES
SEE ALSO
TraceDiff
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Trace_dump
NAME
SYNOPSIS
DESCRIPTION
SEE ALSO
Vector_clip
NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXAMPLES
NOTES
SEE ALSO
Index
References
Copyright
Publications
Index
Master Index