The Artemis Manual


Copyright © 1999-2019 by Genome Research Limited


This document describes release v18.0.0 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


The Artemis Manual 1

Chapter 1. Introduction to Artemis. 1

What is Artemis?. 1

System Requirements. 1

Getting and Installing Artemis. 1

Installation Instructions for UNIX and GNU/Linux. 1

Installation Instructions for MacOSX.. 1

Installation Instructions for Windows. 1

Sequence and Annotation File Formats. 1

Concepts. 1

The "Entry". 1

EMBL/Genbank Features. 1

EMBL/Genbank Feature Keys. 1

EMBL/Genbank Feature Qualifiers. 1

"Tab" Files or "Table" Files. 1

The Active Entries. 1

The Default Entry. 1

Feature Segments. 1

The Selection. 1

Feature Colours. 1

Contributions and Suggestions. 1

Distribution Conditions and Acknowledgments. 1

Copyright Notice. 1

Chapter 2. Starting Artemis. 1

Running Artemis on UNIX and GNU/Linux Systems. 1

UNIX Command Line Arguments for Artemis. 1

-options. 1

-Xmsn -Xmxn. 1

-Dblack_belt_mode=false. 1

-Doffset=10000. 1

-Duserplot=pathToFile. 1

-Dloguserplot=pathToFile. 1

-Dbam=pathToFile. 1

-Dbam1=pathToFile1 -Dbam2=pathToFile2. 1

-DbamClone=n. 1

-Dshow_snps. 1

-Dshow_snp_plot 1

-Dshow_cov_plot 1

-Dchado="hostname:port/database?username". 1

-Dread_only. 1

-Dshow_forward_lines=false. 1

-Dshow_reverse_lines=false. 1

Running Artemis on Macintosh Systems. 1

Running Artemis on Windows Systems. 1

The Artemis Launch Window.. 1

The File Menu. 1

Open Project Manager ... 1

Open File Manager ... 1

Open SSH File Manager ... 1

Open ... 1

Open from EBI - Dbfetch ... 1

Quit 1

The Options Menu. 1

Re-read Options. 1

Enable Direct Editing. 1

Genetic Code Tables. 1

Black Belt Mode. 1

Highlight Active Entry. 1

Show Log Window.. 1

Hide Log Window.. 1

Chapter 3. The Artemis Main Window.. 1

Overview of the Entry Edit Window.. 1

A breakdown of the main Artemis edit window.. 1

The File Menu. 1

Show File Manager ... 1

Read An Entry ... 1

Read Entry Into. 1

Read BAM / CRAM / VCF ... 1

Save Default Entry. 1

Save An Entry. 1

Save An Entry As. 1

New File. 1

EMBL Format 1

GENBANK Format 1

Sequin Table Format 1

GFF Format 1

EMBL Submission Format 1

Save All Entries. 1

Write. 1

Amino Acids Of Selected Features. 1

PIR Database Of Selected Features. 1

Bases Of Selection. 1

Upstream Bases Of Selection. 1

Downstream Bases Of Selection. 1

All Bases. 1

Codon Usage of Selected Features. 1

Clone This Window.. 1

Save As Image Files (png/svg) 1

Print 1

Print Preview.. 1

Preferences. 1

Close. 1

The Entries Menu. 1

Set Name Of Entry. 1

Set Default Entry. 1

Remove An Entry. 1

Remove Active Entries. 1

Deactivate All Entries. 1

The Select Menu. 1

Feature Selector ... 1

All 1

All Bases. 1

Select All Features in Non-matching Regions. 1

None. 1

By Key. 1

CDS Features. 1

Same Key. 1

Open Reading Frame. 1

Features Overlapping Selection. 1

Features Within Selection. 1

Base Range ... 1

Feature AA Range ... 1

Toggle Selection. 1

The View Menu. 1

Selected Features. 1

Selection. 1

Search Results. 1

CDS Genes And Products. 1

Feature Filters. 1

Suspicious Start Codons ... 1

Suspicious Stop Codons ... 1

Non EMBL Keys ... 1

Duplicated Features ... 1

Overlapping CDS Features ... 1

Features Missing Required Qualifiers ... 1

Filter By Key ... 1

Selected Features ... 1

Overview.. 1

Sequence Statistics. 1

Feature Statistics. 1

Forward Strand Overview.. 1

Reverse Strand Overview.. 1

Feature Bases. 1

Feature Bases As FASTA.. 1

Feature Amino Acids As FASTA.. 1

Feature Statistics. 1

Feature Plots. 1

The Goto Menu. 1

Navigator ... 1

Start of Selection. 1

End of Selection. 1

Feature Start 1

Feature End. 1

Start of Sequence. 1

End of Sequence. 1

Feature Base Position ... 1

Feature Amino Acid ... 1

The Edit Menu. 1

Undo. 1

Redo. 1

Selected Features in Editor 1

Subsequence (and Features) 1

Find Or Replace Qualifier Text 1

Qualifier(s) of Selected Feature. 1

Change ... 1

Remove ... 1

Convert ... 1

Selected Feature(s) 1

Duplicate. 1

Merge. 1

Unmerge. 1

Unmerge All Segments. 1

Delete. 1

Delete Exons. 1

Remove Introns. 1

Move Selected Features To. 1

Copy Selected Features To. 1

Trim Selected Features. 1

To Met 1

To Any. 1

To Next Met 1

To Next Any. 1

Extend Selected Features. 1

To Previous Stop Codon. 1

To Next Stop Codon. 1

To Next Stop Codon and Fix. 1

Fix Stop Codons. 1

Automatically Create Gene Names. 1

Fix Gene Names. 1

Bases. 1

Reverse And Complement 1

Reverse And Complement Selected Contig. 1

Delete Selected Bases. 1

Add Bases At Selection. 1

Add Bases From File ... 1

Replace Bases At Selection. 1

Contig Reordering ... 1

Header Of Default Entry. 1

The Create Menu. 1

New Feature. 1

Feature From Base Range. 1

Intergenic Features. 1

Features From Non-matching Regions. 1

New Entry. 1

Mark Open Reading Frames ... 1

Mark Empty ORFs ... 1

Mark Open Reading Frames In Range ... 1

Mark From Pattern ... 1

Mark Ambiguities. 1

The Run Menu. 1

Configuring the Run Menu. 1

Searching and Using Local Sequence Databases for Mac OSX.. 1

The Graph Menu. 1

Hide All Graphs. 1

Add Usage Plots ... 1

Add User Plot ... 1

GC Content (%) 1

GC Content (%) With 2.5 SD Cutoff 1

AG Content (%) 1

GC Frame Plot 1

Correlation Scores. 1

Reverse Correlation Scores. 1

GC Deviation (G-C)/(G+C) 1

AT Deviation (A-T)/(A+T) 1

Karlin Signature Difference. 1

Cumulative AT Skew and Cumulative GC Skew.. 1

Positional Asymmetry. 1

Informational Entropy. 1

Scaled Chi Square. 1

Mutational Response Index. 1

Effective Codon Number 1

Intrinsic Codon Deviation Index. 1

The Display Menu. 1

Show Entry Buttons. 1

Show Base View.. 1

Show Feature List 1

The Entry Button Line. 1

The Overview and DNA Views. 1

Changing the Selection from a View Window.. 1

Other Mouse Controlled Functions. 1

The Pop-up Menu. 1

Pop-up Menu Functions. 1

Toggle Buttons. 1

Scrolling The View.. 1

Changing The Scale. 1

"Direct Editing". 1

The Feature List 1

Changing the Selection from the Feature List 1

Other Mouse Controlled Functions. 1

The Pop-up Menu. 1

Save List to File. 1

Show Selected Qualifier 1

Show Correlation Scores. 1

Show Gene Names. 1

Show Qualifiers. 1

Show Product 1

Scrolling The List 1

Graphs and Plots. 1

Annotation Validation. 1

How to Run Validation Checks. 1

Validation Checks For All File Types. 1

Validation Checks For GFF3. 1

Validation Report 1

Notes on Using The Mouse. 1

Chapter 4. Project File Manager. 1

Overview.. 1

Using the Project File Manager 1

Chapter 5. Secure Shell (SSH) Plugin To Artemis. 1

Overview of the SSH Plugin. 1

Login In. 1

Setting up a SSH tunnel 1

Using Putty to Set Up A Tunnel 1

Chapter 6. Artemis Configuration Options. 1

The Options File. 1

Artemis Option Descriptions. 1

font_size. 1

font_name. 1

base_plot_height 1

feature_plot_height 1

draw_feature_borders. 1

show_forward_lines. 1

show_reverse_lines. 1

draw_feature_arrows. 1

overview_feature_labels. 1

overview_one_line_per_entry. 1

show_list 1

show_base_view.. 1

features_on_frame_lines. 1

frame_line_features. 1

feature_labels. 1

one_line_per_entry. 1

genetic_codes. 1

translation_table_1. 1

extra_keys. 1

extra_qualifiers. 1

common_keys. 1

hyperlinks. 1

undo_levels. 1

minimum_orf_size. 1

direct_edit 1

feature_dna_programs. 1

feature_protein_programs. 1

ncbi_dna_search. 1

ncbi_protein_search. 1

Setting Colours. 1

Options For Plots and Graphs. 1

Options For A Chado Database. 1

chado_exon_model 1

chado_transcript 1

chado_servers. 1

Options File Format 1

An Example Options File. 1


List of Tables

3-1. IUB Base Codes






Chapter 1. Introduction to Artemis


What is Artemis?


Artemis is a DNA sequence viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL or GENBANK format sequences and feature tables, and can work on sequences of any size.


On Unix and GNU/Linux systems, given an EMBL accession number Artemis also can read an entry directly from the EBI using Dbfetch. This feature is still experimental, but copes well with straightforward entries (see the section called Open from EBI - Dbfetch ... in Chapter 2 ).


For more information on Artemis go to the Artemis web pages.



System Requirements


Artemis will run on any machine that has a recent version of Java. This version of Artemis requires Java 9 at least and preferably Java 11. See the section called Getting and Installing Artemis for details on how to get Java.






Getting and Installing Artemis


The most up to date version of Artemis is always available from the Artemis web pages. It’s also available bundled with Java from Bioconda for Mac OSX or UNIX based systems.





Installing Java


Before installing Artemis you will need to make sure you have Java installed. The previous v17.0.1 version of Artemis required Java 1.8 to run. All subsequent recent versions from v18.0.0 onwards require a minimum of Java 9 and preferably Java 11.


The licensing for Java has recently changed and Oracle now offers two flavours – one free GPL licensed GA OpenJDK and one commercial build that requires a subscription for production use. The default option should be the open JDK, but this choice may be dependent upon your organisation so check with your administrator if necessary.


There are a number of ways to install the OpenJDK Java. The easiest is via the AdoptOpenJDK web site - just select the OpenJDK version and Hotspot options for the relevant platform and you’re done.


Other options include Homebrew for Mac OSX or apt on Linux. The current Java 11 version can always be obtained from Select the relevant download link for your operating system, from the Build section of the page. You will generally need administrator privileges for your machine, to successfully install Java.

The download files are either .tar.gz or .zip archives, dependent on operating system. Double-clicking on the downloaded file will usually extract the contents. They may also be extracted on the command line using

$ tar xvf openjdk-11*_bin.tar.gz


$ unzip openjdk-11*

The uncompressed folder will be named similar to jdk-VersionNumber.jdk, e.g. jdk-11.0.1.jdk.

Some good advice on installation can be found in the following articles:

For Ubuntu:


For Mac OS X:

For Windows: See the first answer in


·      For Linux, copy the uncompressed folder into /usr/lib/jvm. Alternatively, use apt or similar, for example:

sudo apt update

sudo apt install default-jdk

java -version

·      For Macs, you will need to copy the uncompressed folder to your /Library/Java/JavaVirtualMachines/ folder since this is the standard location for Java installs, and add the following to your profile (e.g. .bashrc file):

export JAVA_HOME=”/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home”

export PATH="$JAVA_HOME/bin:$PATH"

·      For Windows, make a new “Java” folder under C:\Program Files and copy the uncompressed folder into it. Now Create a new JAVA_HOME environment variable using the Windows Control Panel “System” program. Set it to the path of your newly installed Java folder, e.g. C:\Program Files\Java\jdk-11.0.1.jdk. Now edit the PATH environment variable value and add %JAVA_HOME%\bin: to the start of it. You should now be able to bring up a DOS cmd window and run “java -version” in it, which should show the correct version, e.g. Java 11.




Installation Instructions for UNIX and GNU/Linux


Change directory to the directory you wish to install the Artemis software in. We will use ~/ in this example and in the next chapter.


Uncompress and untar the artemis-unix-release-{version}.tar.gz or artemis-unix-release-{version}.zip file. On UNIX the command for the v18.0.0 release would be:


tar zxf artemis-unix-release-18.0.0.tar.gz


This will create a directory called ~/artemis which will contain all the files necessary for running Artemis and associated tools.


For instructions on how to run Artemis on UNIX and GNU/Linux once the archive is unpacked see the section called Running Artemis on UNIX and GNU/Linux Systems in Chapter 2 .




Installation Instructions for MacOSX


For MacOSX users, an archive artemis-macosx-release-{version}.dmg.gz disk image is provided. Your Mac may uncompress this automatically on download. If not it can be uncompressed by double-clicking on it or by using gunzip, e.g. for the v18.0.0 release:


gunzip artemis-macosx-release-18.0.0.dmg.gz


Alternatively, try the StuffIt Expander app. Double-click on any file ending in ".gz" and StuffIt Expander will be launched to uncompress that file.


The uncompressed disk image file artemis-macosx-release-{version}.dmg can be mounted by double clicking on it. The mounted image, "Artemis_Tools", can then be opened and the software contents displayed by clicking on it.


There’s also an artemis-macosx-chado-release-{version}.dmg disk image that will start up Artemis with a Chado connection window displayed, if you wish to work connected to a Chado database. This is installed in exactly the same way.


For instructions on how to run Artemis on Mac OSX once it is unpacked see the section called Running Artemis on Macintosh Systems.





Installation Instructions for Windows


On Windows systems, installing Artemis is as simple as downloading the artemis-windows-release-{version}.zip file to an appropriate place (such as the desktop or the Programs folder).  Unzip the file using WinZip or equivalent. The unzipped folder will contain the Artemis tool set executable .jar files.


For instructions on how to run Artemis on Windows once it is unpacked see the section called Running Artemis on Windows Systems.





Sequence and Annotation File Formats


Artemis reads in the common sequence and annotation file formats. As larger data sets become more common it is now possible to index some of these formats (FASTA and GFF3) to speed up and improve the performance of Artemis. Artemis can read the following sequence and annotation file formats. As discussed in the next section these can be read individually or as a combination of different annotation files being read in and overlaid on the same sequence.


     EMBL format.


     GenBank format.


     GFF3 format. The file can contain both the sequence and annotation or the GFF can just be the feature annotation and be read in as a seperate entry and overlaid onto another entry containing the sequence.


     FASTA nucleotide sequence files can be one of the following:


      Single FASTA sequence.


      Multiple FASTA sequence. The sequences are concatenated together when opened in



      Indexed FASTA files can be read in. The files are indexed using SAMtools:


samtools faidx ref.fasta



A drop down menu of the sequences in the Entry toolbar (see the section called A breakdown of the main Artemis edit window in Chapter 3) at the top can then be used to select the sequence to view.


     Indexed GFF3 format. This can be read in and overlaid onto an indexed FASTA file. The indexed GFF3 file contains the feature annotations. To index the GFF first sort and bgzip the file and then use tabix with "-p gff" option (see the tabix manual):


(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip >



tabix -p gff sorted.gff.gz



A drop down menu of the sequences in the Entry toolbar (see the section called A breakdown of the main Artemis edit window in Chapter 3) at the top can then used to select the sequence to view. Using indexed FASTA and indexed GFF files improves the memory management and enables large genomes to be viewed. Note that as it is indexed the sequence and annotation are read-only and cannot be edited. When there are many contigs to select from it can be easier to display the one of interest by typing the name into the drop down list.


     The output of MSPcrunch. MSPcrunch must be run with the -x or -d flags.


     The output of blastall version 2.2.2 or better. blastall must be run with the -m 8 flag which generates one line of information per HSP. Note that currently Artemis displays each Blast HSP as a separate feature rather than displaying each BLAST hit as a feature.







Here are some general concepts about Artemis that may make the rest of this manual clearer.





The "Entry"


An "entry" in Artemis-speak is not necessarily a complete EMBL or GENBANK entry. In most places in this manual when we refer to an entry we mean a file that contains just the feature table lines (the FT lines) of an EMBL/GENBANK entry (see the section called "Tab" Files or "Table" Files). After loading a sequence and opening an entry edit window (see the section called Open ... in Chapter 2) it is then possible to overlay many feature tables (see the section called Read an Entry.. in Chapter 3). Each of these feature table files is called an entry by Artemis and it's features are kept separate from those of other entries.


This meaning of the word "entry" is used by most of the items in the File menu (see the section called The File Menu in Chapter 3) and by the items in the Entry menu (see the section called The Entries Menu in Chapter 3).



EMBL/Genbank Features


A "feature" in an EMBL or Genbank file is a region of DNA that has been annotated with a key/type (see the section called EMBL/Genbank Feature Keys) and zero or more qualifiers (see the section called EMBL/Genbank Feature Qualifiers). In an EMBL or Genbank formated file the features of a piece of DNA are listed in the feature table section (see the section called "Tab" Files or "Table" Files).




EMBL/Genbank Feature Keys


All EMBL and Genbank features have exactly one "key" assigned to them. The key is the type of the feature. Examples include CDS (a CoDing Sequence), intron and misc_feature (MISCellaneous feature).


The EBI has a list of all possible feature keys.





EMBL/Genbank Feature Qualifiers


The qualifiers of a feature in an EMBL or Genbank file are the notes and extra information about the feature. For example an exon feature might have a /gene="ratC" qualifier, meaning that the exon feature is part of a gene named ratC.


The EBI has a list of all possible feature qualifiers.





"Tab" Files or "Table" Files


An EMBL or Genbank file that only contains a feature table (just FT lines, no sequence or header lines) is called a "table" file, or sometimes just a "tab" file because the often has a name like "".





The Active Entries


All entries in Artemis are considered to be "active" or "inactive". The overview, DNA view and feature list parts of the main window will only display features from active entries. To find out how to set the active and inactive entries see the section called The Entries Menu in Chapter 3.





The Default Entry


Many actions (such as creating features) require an entry to be identified as the source or destination for the action. Some actions, such as "Move Selected Features To ..." in the edit menu, will explicitly ask for

an entry, but some assume that the action refers to a "default entry" that was previously set by the user.


The default entry can be set by using the "Set Default Entry ..." menu item in the Entries menu (see the section called Set Default Entry in Chapter 3) or by using the entry buttons (see the section called The Entry Button Line in Chapter 3).





Feature Segments


The term "segment" in the context of a CDS feature means "exon". We use the term "segment", because non-CDS features (such as misc_feature) can have exon-like parts too, but the term "exon" would be inappropriate in that case.





The Selection


In common with applications like word processors and graphics programs, Artemis allows the user to "select" the objects that the program will act on. The objects to act on in Artemis are features, feature segments or bases. If a feature segment is added to the selection, the feature that contains the segment is implicitly added as well. The current selection can be changed with the Select Menu (see the section called The Select Menu in Chapter 3) or using the mouse (see the section called Changing the Selection from a View Window in Chapter 3) and the section called Changing the Selection from the Feature List in Chapter 3).





Feature Colours


Each feature displayed in Artemis can be given a colour. The available colours are set in the options file (see Chapter 6) and are assigned to a feature by adding a /colour qualifier (see the section called Selected Features in Editor in Chapter 3). Currently there are two ways of specifying feature colours. The first way uses a single number. For example red is colour 2, so adding /colour=2 as a feature qualifier will make that feature red. The second way is to specify the red, green and blue components of the colour. Each of the components can take values from 0 to 255, with 255 being the most intense. For example /colour=255 0 0 is another way to give a feature the colour red. If no /colour qualifier is set for a feature a default colour is used (the default colours are also specified in the options file).





Contributions and Suggestions


We welcome contributions to Artemis, bug reports from users and suggestions for new features. An email discussion list has been set up for this purpose. To join, send a message to '' with 'subscribe artemis-users' in the body (not the subject). Announcements will also be sent to this list.




Distribution Conditions and Acknowledgments


Artemis may be freely distributed under the terms of the GNU General Public License. See the section called Copyright Notice for the full text of the license.


The development of Artemis is funded by the Wellcome Trust through its support of the Pathogen Informatics Group at The Sanger Institute.





Copyright Notice



Version 2, June 1991


Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA


Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.




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When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.


To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.


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This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.


8.  If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License.


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Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.


10.  If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.













Chapter 2. Starting Artemis


Running Artemis on UNIX and GNU/Linux Systems


On Unix and GNU/Linux the easiest way to run the program is to run the script called art in the Artemis installation directory (see the section called Getting and Installing Artemis in Chapter 1), like this:




If all goes well you will be presented with a small window with three menus. See The Artemis Launch Window to find out what to do next.


Alternatively you can start Artemis with the name of a sequence file or embl file eg:


artemis/art artemis/etc/c1215.embl


Or if you have a sequence file and extra feature table files you can read them all with a command like this (the example file is the result of a BLASTN search against EMBL which has been converted to feature table format):


artemis/art artemis/etc/c1215.embl + artemis/etc/


Note that any number of feature files can be read by listing them after the plus sign. The "+" must be surrounded by spaces.


See the section called UNIX Command Line Arguments for Artemis for a list of the other possible arguments. Also to see a summary of the options type:


artemis/art -help





UNIX Command Line Arguments for Artemis


As well as the listing file names on the command line, the following switches are available to UNIX users:







This option instructs Artemis to read an extra file of options after reading the standard options. (See the section called The Options File in Chapter 6 for more about the Artemis options file.)


For example -options ./new_options will instruct Artemis to read new_options in the current directory as an options file.





-Xmsn -Xmxn


Use -Xmsn to specify the initial size, in bytes, of the memory allocation pool. This value must be a multiple of 1024 greater than 1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.


Use -Xmxn to specify the maximum size, in bytes, of the memory allocation pool. This value must a multiple of 1024 greater than 2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.







If this is set to false then warning messages are kept to a minimum.







This sets the base position that Artemis opens at, e.g. 10000.






This can be used to open userplots from the command line. The paths are comma separated to open multiple plots (-Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2').







This is the same as the above userplot option except that the log transform of the data is plotted.







This can be used to open BAM/CRAM files and/or VCF/BCF files (see the section called Read BAM / CRAM / VCF ... in Chapter 3 for more about the using these file types). This can take a path name to a file or an HTTP address. Multiple files can be comma separated.





-Dbam1=pathToFile1 -Dbam2=pathToFile2


The following will open BAM/CRAM files in separate panels (using -Dbam[1,2,3...]):


art -Dbam1=fileA.bam -Dbam2=fileB.bam







Multiple BAM/CRAM panels can be opened using the bamClone flag this is used with the -Dbam flag:


art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n


(where n is an integer greater than 1). All BAM/CRAM files are then shown in each panel.







Show SNP marks in BAM/CRAM panels.






Automatically open SNP plots for BAM/CRAM files that are opened.







Automatically open coverage plots for BAM/CRAM files that are opened.







This is used to get Artemis to look for the database. The address of the database (hostname, port and name) can be conveniently included (e.g. -Dchado="") and these details are then the default database address in the popup login window.







For a read only chado connection -Dread_only is specified on the command line (e.g. art -Dchado="" -Dread_only).







Hide/show forward frame lines.







Hide/show reverse frame lines.





Running Artemis on Macintosh Systems


On MacOSX machines Artemis can be started by double clicking on the Artemis icon. The icon can be added to the dock by dragging it from a 'Finder' window and dropping it onto the position in the dock you want it. In addition sequence files (with gff,gff3,embl,EMBL,genbank,gbk,fasta,fa,seq file name extensions) can be dragged and dropped on to the Artemis application image to open them up.


To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Towards the bottom of the file you will see these lines:






Changing the value after -mx will change the max memory used by Artemis. The default is 2Gb.


Similarly, to start Artemis with a particular default Chado database connection you can add a <string>-Dchado=”connection string”</string> line to the above section (see -Dchado="hostname:port/database?username").





Running Artemis on Windows Systems


On Windows, Artemis can be started by double clicking on the artemis.jar icon, and similarly for the other tools.


If it fails to start, then it’s likely that either Java is not installed properly, or another program has hijacked the .jar file association (this could happen if a .jar was previously opened with Notepad for example, and then that association saved as the default). To check that Java is installed, run up a DOS window (Type cmd in the run menu) and then in the DOS window type java -version – this should display the correct Java version number.


To fix an incorrect file association, provides some helpful information.


A backstop solution that always works is to create a text file in Notepad [or an alias] with the following line in it:


java -jar artemis.jar



Save this file as artemis.bat in the same folder as the jar file (i.e. change the default .txt file extension to .bat before saving). Then just double click on that file instead of the .jar.


The same can be done for the other tools, e.g. for BamView create a bamview.bat containing: java –jar bamview.jar




The Artemis Launch Window


This is the first window that opens when you start Artemis. The menus at the top of this window allow you to read a new sequence or embl entry.






The File Menu



Open Project Manager ...


This opens up the Project File Manager which can be used to facilitate launching of groups of files (annotation, userplot, BAM, CRAM, VCF) with a particular sequence. See Chapter 4.





Open File Manager ...


Selecting this shows the files and directories that are in the directory Artemis is launched from. The user home directory and the current working directories are shown and can be navigated.





Open SSH File Manager ...


This opens a window displaying a local file manager at the top and login options to access a remote file system via Secure Shell (SSH). When the login details are typed in and 'Connect' pressed the bottom half of the window will display the other (remote) file system. See Chapter 5 to find out how to use this and how to set up the connection.





Open ...


If you select this menu item a file requester will be displayed which allows you to open a flat file containing an entry. If the file you select is successfully read a new window will open, which shows the

sequence and features for the entry. See Chapter 3 to find out how to use the main window.





Open from EBI - Dbfetch ...


The functions will ask the user for an accession number and then will attempt to read it directly from the EBI using Dbfetch. If all goes well you will be presented with an view/edit window (see Chapter 3).







This menu item will close all windows and then exit the program





The Options Menu



Re-read Options


Choosing this menu item will discard the current options settings and then re-read the options file. Note that changing the font size in the file and then selecting this menu item will only change the font size for new windows, not existing windows. Currently some options are unaffected by this menu item. See the section called Options File Format in Chapter 6 for more information about options.





Enable Direct Editing


This menu item will toggle "direct editing" option. It is off by default because it can have surprising results unless the user is expecting it. See the section on "Direct Editing" in Chapter 3 for more detail about this.





Genetic Code Tables


These options make all the NCBI Genetic Codes available. The default setting is the Standard Code. This setting effects the display of start codons (see the section called Start Codons in Chapter 3) and the "Suspicious Start Codons ..." feature filter (see the section called Suspicious Start Codons ... in Chapter 3).





Black Belt Mode


This is an advanced option that can be used to turn off warning message. This options is displayed if the java property (black_belt_mode) is specified on opening up Artemis, i.e. art -Dblack_belt_mode=yes.





Highlight Active Entry


When this option is on and the "One Line Per Entry" is on (see the section called One Line per Entry in Chapter 3) the line that the active entry is on will be highlighted in yellow.





Show Log Window


Show the log of informational messages from Artemis. Currently the log window is only used on UNIX and GNU/Linux systems to show the output of external programs. This menu item is only available when running Artemis on UNIX or GNU/Linux systems. The logging is controlled by log4j. The file (etc/ in the source distribution) sets the level of logging. This can be used to send the logging information to other places such as a file.





Hide Log Window


Hide the log of informational messages. This menu item is only available when running Artemis on UNIX or GNU/Linux systems.






Chapter 3. The Artemis Main Window



Overview of the Entry Edit Window


This window is the main editing and viewing window. See the section called Open ... in Chapter 2 or the section called Open from EBI - Dbfetch ... in Chapter 2 to find out how to read an entry (and hence open one of these windows).


The following images show a breakdown of the main Artemis edit window.





A breakdown of the main Artemis edit window


















1.     The menus for the main window (described later in this chapter).


2.     A one line summary of the current selection (see the section called The Select Menu and the section called The Selection in Chapter 1 for more).


3.     This line contains one button for each entry that has been loaded. These buttons allow the user to set the default entry (see the section called The Default Entry in Chapter 1 ) and to set the active entries (see the section called The Active Entries in Chapter 1 ). For more detail on operating the buttons see the section called The Entry Button Line .


4.     This shows an overview of the sequence and the features from the active entries. (see the section called The Overview and DNA Views in Chapter 3).


5.     This is called the "DNA view" to distinguish it from the overview, but in fact it operates in a very similar way. (see the section called The Overview and DNA Views in Chapter 3).


6.     A textual summary of the active features. (See the section called The Feature List in Chapter 3).






The File Menu


Most of the items in this menu are used to read and write entries and parts of entries, the exceptions are Clone and Close.





Show File Manager ...


This will open the file manager, or if it is already open will bring it to the foreground. Entries can be dragged from the file manager into the Artemis main window and dropped. When dropped the entry is then read in and displayed.





Read An Entry ...


Read an entry (see the section called The "Entry" in Chapter 1 ), but keep it separate from the others. A new button will be created on the entry button line for the new entry. The new entry will be marked as active (see the section called The Active Entries in Chapter 1 ) and will be the new default entry (see the section called The Default Entry in Chapter 1).


See the section called Sequence and Annotation File Formats in Chapter 1 . This function only reads the feature section of the input file - the sequence (if any) is ignored.





Read Entry Into


Read the features from an entry (see the section called The "Entry" in Chapter 1 ) chosen by the user and then insert them into the entry selected by the user.





Read BAM / CRAM / VCF ...


Artemis can read in and visualise BAM, CRAM, VCF and BCF files. These files need to be indexed as described below. Some examples can be found here.


BAM files need to be sorted and indexed using SAMtools. The index file should be in the same directory as the BAM file. This provides an integrated BamView panel in Artemis, displaying sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded in from here either by selecting each file individually or by selecting a file of path names to the BAM files. The BAM files can be read from a local file system or remotely from an HTTP server.


BamView will look to match the length of the sequence in Artemis with the reference sequence lengths in the BAM file header. It will display a warning when it opens if it finds a matching reference sequence (from these lengths) and changes to displaying the reads for that. The reference sequence for the mapped reads can be changed manually in the drop down list in the toolbar at the top of the BamView.

In the case when the reference sequences are concatenated together into one (e.g. in a multiple FASTA sequence) and the sequence length matches the sum of sequence lengths given in the header of the BAM, Artemis will try to match the names (e.g. locus_tag or label) of the features (e.g. contig or chromosome) against the reference sequence names in the BAM. It will then adjust the read positions accordingly using the start position of the feature.


When open the BamView can be configured via the popup menu which is activated by clicking on the BamView panel. The 'View' menu allows the reads to be displayed in a number of views: stack, strand-stack, paired-stack, inferred size and coverage.


In Artemis the BamView display can be used to calculate the number of reads mapped to the regions covered by selected features. In addition the reads per kilobase per million mapped reads (RPKM) values for selected features can be calculated on the fly. Note this calculation can take a while to complete.


CRAM files can be loaded in a similar fashion to BAMs. They can be created, sorted and indexed using SAMtools.


Variant Call Format (VCF) files can also be read. The VCF files need to be compressed and indexed using bgzip and tabix respectively (see the tabix manual and download page). The compressed file gets read in (e.g. file.vcf.gz) and below are the commands for generating this from a VCF file:


bgzip file.vcf


tabix -p vcf file.vcf.gz



Alternatively a Binary VCF (BCF) can be indexed with BCFtools and read into Artemis or ACT.


As with reading in multiple BAM/CRAM files, it is possible to read a number of (compressed and indexed) VCF files by listing their full paths in a single file. They then get displayed in separate rows in the VCF panel.



For single base changes the colour represents the base it is being changed to, i.e. T black, G blue, A green, C red. There are options available to filter the display by the different types of variants. Right clicking on the VCF panel will display a pop-up menu in which there is a 'Filter...' menu. This opens a window with

check boxes for a number of variant types and properties that can be used to filter on. This can be used to show and hide synonymous, non-synonymous, deletion (grey), insertion (magenta), and multiple allele (orange line with a circle at the top) variants. In this window there is a check box to hide the variants that do not overlap CDS features. There is an option to mark variants that introduce stop codons (into the CDS features) with a circle in the middle of the line that represents the variant. There are also options to filter the variants by various properties such as their quality score (QUAL) or their depth across the samples (DP).


Placing the mouse over a vertical line shows an overview of the variation as a tooltip. Also right clicking over a line then gives an extra option in the pop-up menu to show the details for that variation in a separate window. There are also alternative colouring schemes. It is possible to colour the variants by whether they are synonymous or non-synonymous or by their quality score (the lower the quality the more faded the variant appears).


There is an option to provide an overview of the variant types (e.g. synonymous, non-synonymous, insertion, deletion) for selected features. Also, filtered data can be exported in VCF format, or the reconstructed DNA sequences of variants can be exported in FASTA format for selected features or regions for further analyses. These sequences can be used as input for multiple sequence alignment tools.





Save Default Entry


Save the default entry to the file it came from, unless the entry has been given a new name, in which case the entry is saved to a file with that name. If the entry has no name, Artemis will prompt the user for a new name. [shortcut key: S]





Save An Entry


This item will do the same as "Save Default Entry" for the chosen entry.





Save An Entry As


This sub-menu contains the less frequently used save functions.





New File


Ask for the name of file to save the given entry to. The name of entry (as displayed in the entry button line) will change to the new name.





EMBL Format


This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in EMBL format. Note that currently the header of a GENBANK entry can't be converted to the

equivalent EMBL header (it will be discarded instead).







This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in GENBANK format. Note that currently the header of a EMBL entry can't be converted to the equivalent GENBANK header (it will be discarded instead).





Sequin Table Format


This saves a file in Sequin table format which is used by Sequin.