The Artemis Manual

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


Table of Contents
1. Introduction to Artemis
What is Artemis?
Requirements
Getting Artemis
How to install Artemis
Installation Instructions for UNIX
Installation Instructions for Windows
Contributions and Suggestions
Distribution Conditions and Acknowledgments
Copyright Notice
2. Starting Artemis
Running Artemis on UNIX Systems
Running Artemis on MSDOS/Windows Systems
The Artemis Launch Window
The File Menu
The Options Menu
Entry Edit Concepts
The "Entry"
"Tab" Files or "Table" Files
The Active Entries
The Default Entry
Feature Segments
The Selection
Feature Colours
The Options File
font_size
minimum_orf_size
extra_keys
extra_qualifiers
common_keys
Setting Colours
An Example Options File
3. The Artemis Main Window
Overview of the Entry Edit Window
A breakdown of the main Artemis edit window
The File Menu
Read Features
Read An Entry
Clone This Window
Save Default Entry
Save An Entry ...
Save An Entry As ...
Save An Entry As EMBL ...
Save All Entries
Set Default Entry ...
Set Name Of Default Entry
Close
The Select Menu
Select All
Select None
Select By Type
Select CDS Features
Select Same Type
Select Open Reading Frame
Select Same Type
Toggle Selection
The View Menu
View Selected Features
View Selection
Show Overview
View Feature Bases
View Feature Amino Acids
Show Feature Statistics
Show Feature Plots
The Goto Menu
Goto ...
Goto Start of Selection
Goto End of Selection
Goto Feature Start
Goto Feature End
Goto Start of Sequence
Goto End of Sequence
Goto Feature Base Position
Goto Feature Amino Acid
The Edit Menu
Edit Selected Features
Raw Edit Selected Features
Duplicate Selected Features
Delete Selected Features
Delete An Entry ...
Move Selected Features To ...
Copy Selected Features To ...
Trim Selected Features To Met
Trim Selected Features To 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 Open Reading Frames In Range
Mark From Pattern
The Write Menu
Bases Of Selection
Amino Acids Of Selected Features
PIR Database Of Selected Features
Upstream Bases Of Selection
Downstream Bases Of Selection
Write All Bases (Raw)
Write All Bases (Fasta)
Write All Bases (EMBL)
Write All Bases (GENBANK)
Write Codon Usage of Selected Features
The Run Menu
The Display Menu
Show Base View
Show Feature List
Add Usage Plots ...
GC Content (%)
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
"Direct Editing"
Changing the Selection
Other Mouse Controlled Functions
The Pop-up Menu
Scrolling The View
Changing The Scale
The Feature List
Changing the Selection
The Pop-up Menu
Scrolling The List
Graphs and Plots
Notes on Using The Mouse