The Artemis Manual

Copyright © 1999, 2000 by Genome Research Limited

This document describes the Artemis DNA sequence viewer and sequence annotation tool.

Table of Contents
1. Introduction to Artemis
What is Artemis?
System Requirements
Getting and Installing Artemis
Installation Instructions for UNIX
Installation Instructions for Macintosh Systems
Installation Instructions for Windows
Concepts
The "Entry"
"Tab" Files or "Table" Files
The Active Entries
The Default Entry
Feature Segments
The Selection
Feature Colours
Contributions and Suggestions
Distribution Conditions and Acknowledgments
Copyright Notice
2. Starting Artemis
Running Artemis on UNIX Systems
UNIX Command Line Arguments for Artemis
-quiet
-options
Running Artemis on Windows Systems
Running Artemis on Macintosh Systems
The Artemis Launch Window
The File Menu
The Options Menu
3. The Artemis Main Window
Overview of the Entry Edit Window
A breakdown of the main Artemis edit window
The File Menu
Read An Entry
Read Features Into
Clone This Window
Save Default Entry
Save An Entry
Save An Entry As
Save All Entries
Close
The Entries Menu
Set Name Of Default Entry
Set Default Entry
Remove An Entry
Deactivate All Entries
The Select Menu
Feature Selector ...
All
All Bases
None
By Key
CDS Features
Same Key
Open Reading Frame
Features in Range
Base Range ...
Feature AA Range ...
Toggle Selection
The View Menu
View Selected Features
View Selection
Search Results
Show CDS Genes And Products
Feature Filters
Show Overview
Show Forward Strand Overview
Show Reverse Strand Overview
View Feature Bases
View Feature Bases As FASTA
View Feature Amino Acids
View Feature Amino Acids As FASTA
Show Feature Statistics
Show Feature Plots
The Goto Menu
Navigator ...
Start of Selection
End of Selection
Feature Start
Feature End
Start of Sequence
End of Sequence
Feature Base Position ...
Feature Amino Acid ...
The Edit Menu
Edit Selected Features
Edit Subsequence (and Features)
Edit Header Of Default Entry
Duplicate Selected Features
Merge Selected Features
Delete Selected Features
Delete Selected Exons
Move Selected Features To
Copy Selected Features To
Trim Selected Features To Met
Trim Selected Features To Any
Trim Selected Features To Next Met
Trim Selected Features To Next Any
Automatically Create Gene Names
Fix Stop Codons
Reverse And Complement
Delete Selected Bases
Add Bases At Selection
The Create Menu
New Feature
Create Feature From Base Range
New Entry
Mark Open Reading Frames ...
Mark Empty ORFs ...
Mark Open Reading Frames In Range ...
Mark From Pattern ...
Mark Ambiguities
The Write Menu
Amino Acids Of Selected Features
PIR Database Of Selected Features
Bases Of Selection
Upstream Bases Of Selection
Downstream Bases Of Selection
Write All Bases (Raw)
Write Codon Usage of Selected Features
The Run Menu
Configuring the Run Menu
The Display Menu
Show Entry Buttons
Show Base View
Show Feature List
Hide All Graphs
Add Usage Plots ...
GC Content (%)
GC Content (%) With 2.5 SD Cutoff
AG Content (%)
GC Frame Plot
Correlation Scores
Reverse Correlation Scores
GC Deviation (G-C)/(G+C)
AT Deviation (A-T)/(A+T)
The Entry Button Line
The Overview and DNA Views
Changing the Selection from a View Window
Other Mouse Controlled Functions
The Pop-up Menu
Scrolling The View
Changing The Scale
"Direct Editing"
The Feature List
Changing the Selection from the Feature List
Other Mouse Controlled Functions
The Pop-up Menu
Scrolling The List
Graphs and Plots
Notes on Using The Mouse
4. Artemis Configuration Options
The Options File
Artemis Option Descriptions
font_size
minimum_orf_size
start_codons
translation_table
extra_keys
extra_qualifiers
common_keys
feature_dna_programs
feature_protein_programs
Setting Colours
Options For Plots and Graphs
Options File Format
An Example Options File
List of Tables
3-1. IUB Base Codes
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  Introduction to Artemis