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User Guide to SeqNinja — 18.0
18.0
Table of Contents
Home Page
User Guide to SeqNinja — 18.0
User Guide to SeqNinja — 18.0
Welcome to SeqNinja
SeqNinja with GUI Help
Getting Started with SeqNinja
SeqNinja Tutorials
Tutorial 1: Inserting bases into an existing sequence
Part A: Setting up preferences
Part B: Inserting the bases
Part C: Running the script
Tutorial 2: Extracting features as sequences and translating them
Part A: Defining sequence variables
Part B: Adding a gene extraction step
Part C: Translating the extracted genes
Part D: Extracting and translating features using an alternative method
Tutorial 3: Reverse complementing and translating a sub-range of a sequence
Part A: Defining a sub-range of a sequence
Part B: Adding the reverse complement step
Part C: Adding the translation step
Create and Open Projects
The SeqNinja Interface
The SeqNinja project
Welcome screen
Script views
Visual view
Components of the visual view
Right-click functionality in the Visual view
Text view
Console panel
Toolbar
Templates panel
Blank Script
Add Features
Change Sequence Origin
Collect Sequences
Concatenate Sequences
Convert File Type
Create Insertion
Extract Features as Sequences
Map Features
Features screen
Sequences screen
Options screen
Output screen
Map Features output files
Feature mapping comparison: MegAlign Pro vs. SeqNinja
Modify Sequence(s)
Reverse Complement Sequence(s)
Sample Sequences
Split Sequences
Translate
Write Features
Toolkit panel
Settings section
Converting between annotated and featureless formats
Sequences section
Write to Results File
Define Sequence Variable
Add Sub-Range
Add Sequence File
Add Sequence Text
Add Sequence Variable
Functions section
Annotate
Collect Sequences
Cut Sequence(s)
Extract Features Function
Reverse Complement
Sample Sequences
Strip Metadata
Translate
Label as DNA / RNA / Protein
Label as Circular / Linear
Other Section
Add Comment
Print to Console
Split Sequence Set
Define Integer Variable
Split the SeqNinja screen
Hide, show and change the sizes of items in the SeqNinja interface
Work with Sequences
Add and modify a sequence
Set sequence ends
Work with Features
Work with Scripts
Specify file paths
Specify output format and location
Perform multiple calculations
Use file patterns
Use escape codes
Use setting substitution
Use editing commands
Run a script
Stop running a script
Access run results
Use drag & drop
Save, Close and Exit
Miscellaneous
Set preferences
Default Run Options
Editor
Help
Internet
Temporary Files
Turn off usage logging
Clean cached files on startup
SeqNinja Command-Line Help
Getting Started with SeqNinja Command-Line
Command-Line Options
The SeqNinja Language
Escape codes
File patterns
Settings
Integral expressions
Sequence expressions and assignments
Sequence filenames, literal sequences and variables
Multi-sequence files and expressions
Sequence fragments
Sequence concatenation
Sequence functions
Actions
Convert Between Annotated and Featureless Formats
Use Setting Substitution
Edit in the SeqNinja Shell
Perform Multiple Calculations
Example Scripts
Add segments of literal sequence to every sequence in a set
Collect sequences with certain attributes into a single file
Concatenate and de-concatenate contigs for gene finding
Convert one version of a sequence to another
Divide a genome into pieces of a specified length & with a specified overlap
Extract annotated features from a genome
Extract segments from a sequence
Extract a specific set of genes or proteins from multiple genomes
Insert a missing base into a sequence
Reverse complement a sequence
Split a multi-sequence file into individual files
Appendix
Supported file types
Change the default application for opening files
IUPAC codes for amino acids
IUPAC codes for nucleotides
Create a script to use as MegAlign Pro input
Research references
Download as PDF
Miscellaneous
Save, Close and Exit
Set preferences
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