The Artemis Manual

This document describes release 8 of Artemis a DNA sequence viewer and sequence annotation tool.

Artemis is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

For the full text of the license see the section called Copyright Notice in Chapter 1.


Table of Contents
1. Introduction to Artemis
What is Artemis?
System Requirements
Getting and Installing Artemis
Installing Java
Installation Instructions for UNIX and GNU/Linux
Installation Instructions for MacOSX
Installation Instructions for Windows
Concepts
The "Entry"
EMBL/Genbank Features
EMBL/Genbank Feature Keys
EMBL/Genbank Feature Qualifiers
"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 and GNU/Linux Systems
UNIX Command Line Arguments for Artemis
-quiet
-options
-fast
-Xmsn -Xmxn
Running Artemis on Macintosh Systems
Running Artemis on Windows 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
Show File Manager ...
Read An Entry ...
Read Entry Into
Save Default Entry
Save An Entry
Save An Entry As
Save All Entries
Clone This Window
Print Image Files (PNG/JPEG)
Print Preview
Preferences
Close
The Entries Menu
Set Name Of Entry
Set Default Entry
Remove An Entry
Remove Active Entries
Deactivate All Entries
The Select Menu
Feature Selector ...
All
All Bases
Select All Features in Non-matching Regions
None
By Key
CDS Features
Same Key
Open Reading Frame
Features Overlapping Selection
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
Undo
Edit Selected Features
Edit Subsequence (and Features)
Edit Header Of Default Entry
Change Qualifiers of Selected ...
Remove Qualifiers of Selected ...
Duplicate Selected Features
Merge Selected Features
Unmerge Selected Feature
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
Extend to Previous Stop Codon
Extend to Next Stop Codon
Fix Stop Codons
Automatically Create Gene Names
Fix Gene Names
Reverse And Complement
Reverse And Complement Selected Contig
Delete Selected Bases
Add Bases At Selection
Add Bases From File ...
Contig Reordering ...
The Create Menu
New Feature
Create Feature From Base Range
Create Features From Non-matching Regions
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
Write Codon Usage of Selected Features
The Run Menu
Configuring the Run Menu
The Graph Menu
Hide All Graphs
Add Usage Plots ...
Add User Plot ...
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)
Karlin Signature Difference
Cumulative AT Skew and Cumulative GC Skew
Positional Asymmetry
Informational Entropy
Scaled Chi Square
Mutational Response Index
Effective Codon Number
Intrinsic Codon Deviation Index
The Display Menu
Show Entry Buttons
Show Base View
Show Feature List
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. Secure Shell (SSH) Plugin To Artemis
Overview of the SSH Plugin
Loggin In
Setting up a SSH tunnel
Using Putty to Set Up A Tunnel
Using the SSH connection to run Fasta and BLAST
Configuring Searches to be run via SSH
5. Artemis Configuration Options
The Options File
Artemis Option Descriptions
font_size
font_name
base_plot_height
feature_plot_height
draw_feature_borders
draw_feature_arrows
overview_feature_labels
overview_one_line_per_entry
show_list
show_base_view
features_on_frame_lines
feature_labels
one_line_per_entry
organism_type
genetic_codes
translation_table_1
extra_keys
extra_qualifiers
common_keys
undo_levels
minimum_orf_size
direct_edit
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