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 ....................................................................................................................... 10 What is Artemis? ................................................................................................................................................... 10 System Requirements ............................................................................................................................................ 10 Getting and Installing Artemis .............................................................................................................................. 10 Installation Instructions for UNIX and GNU/Linux ......................................................................................... 12 Installation Instructions for MacOSX ............................................................................................................... 12 Installation Instructions for Windows ............................................................................................................... 12 Sequence and Annotation File Formats ................................................................................................................ 13 Concepts ................................................................................................................................................................ 14 The "Entry"........................................................................................................................................................ 14 EMBL/Genbank Features .................................................................................................................................. 14 EMBL/Genbank Feature Keys .......................................................................................................................... 14 EMBL/Genbank Feature Qualifiers .................................................................................................................. 15 "Tab" Files or "Table" Files .............................................................................................................................. 15 The Active Entries ............................................................................................................................................. 15 The Default Entry .............................................................................................................................................. 15 Feature Segments .............................................................................................................................................. 15 The Selection ..................................................................................................................................................... 16 Feature Colours ................................................................................................................................................. 16 Contributions and Suggestions .............................................................................................................................. 16 Distribution Conditions and Acknowledgments ................................................................................................... 16 Copyright Notice ................................................................................................................................................... 17 Chapter 2. Starting Artemis ................................................................................................................................... 22 Running Artemis on UNIX and GNU/Linux Systems .......................................................................................... 22 UNIX Command Line Arguments for Artemis..................................................................................................... 22 -options .............................................................................................................................................................. 22 -Xmsn -Xmxn .................................................................................................................................................... 23 -Dblack_belt_mode=false ................................................................................................................................. 23 -Doffset=10000 ................................................................................................................................................. 23 -Duserplot=pathToFile ...................................................................................................................................... 23 -Dloguserplot=pathToFile ................................................................................................................................. 23 -Dbam=pathToFile ............................................................................................................................................ 23 -Dbam1=pathToFile1 -Dbam2=pathToFile2 .................................................................................................... 24 -DbamClone=n .................................................................................................................................................. 24 -Dshow_snps ..................................................................................................................................................... 24 -Dshow_snp_plot .............................................................................................................................................. 24 -Dshow_cov_plot .............................................................................................................................................. 24 -Dchado="hostname:port/database?username" ................................................................................................. 24 -Dread_only ....................................................................................................................................................... 25 -Dshow_forward_lines=false ............................................................................................................................ 25 -Dshow_reverse_lines=false ............................................................................................................................. 25 Running Artemis on Macintosh Systems .............................................................................................................. 25 Running Artemis on Windows Systems................................................................................................................ 25 The Artemis Launch Window ............................................................................................................................... 26 The File Menu ................................................................................................................................................... 26 Open Project Manager ... ............................................................................................................................... 26 Open File Manager ... .................................................................................................................................... 26 Open SSH File Manager ... ........................................................................................................................... 26 Open ... .......................................................................................................................................................... 27 Open from EBI - Dbfetch ... .......................................................................................................................... 27 Quit ................................................................................................................................................................ 27 The Options Menu ............................................................................................................................................. 27 Re-read Options............................................................................................................................................. 27 Enable Direct Editing .................................................................................................................................... 27 Genetic Code Tables ..................................................................................................................................... 27 Black Belt Mode............................................................................................................................................ 28 Highlight Active Entry .................................................................................................................................. 28 Show Log Window........................................................................................................................................ 28 Hide Log Window ......................................................................................................................................... 28 Chapter 3. The Artemis Main Window ................................................................................................................. 29 Overview of the Entry Edit Window..................................................................................................................... 29 A breakdown of the main Artemis edit window ............................................................................................... 29 The File Menu ....................................................................................................................................................... 30 Show File Manager ... ....................................................................................................................................... 30 Read An Entry ... ............................................................................................................................................... 31 Read Entry Into ................................................................................................................................................. 31 Read BAM / CRAM / VCF ... ........................................................................................................................... 31 Save Default Entry ............................................................................................................................................ 33 Save An Entry ................................................................................................................................................... 33 Save An Entry As .............................................................................................................................................. 33 New File ............................................................................................................................................................ 33 EMBL Format ............................................................................................................................................... 33 GENBANK Format ....................................................................................................................................... 34 Sequin Table Format ..................................................................................................................................... 34 GFF Format ................................................................................................................................................... 34 EMBL Submission Format............................................................................................................................ 34 Save All Entries ................................................................................................................................................. 34 Write .................................................................................................................................................................. 34 Amino Acids Of Selected Features ............................................................................................................... 34 PIR Database Of Selected Features ............................................................................................................... 35 Bases Of Selection ........................................................................................................................................ 35 Upstream Bases Of Selection ........................................................................................................................ 35 Downstream Bases Of Selection ................................................................................................................... 35 All Bases ....................................................................................................................................................... 35 Codon Usage of Selected Features ................................................................................................................ 35 Clone This Window .......................................................................................................................................... 36 Save As Image Files (png/svg).......................................................................................................................... 36 Print ................................................................................................................................................................... 36 Print Preview ..................................................................................................................................................... 36 Preferences ........................................................................................................................................................ 36 Close .................................................................................................................................................................. 36 The Entries Menu .................................................................................................................................................. 37 Set Name Of Entry ............................................................................................................................................ 37 Set Default Entry ............................................................................................................................................... 37 Remove An Entry .............................................................................................................................................. 37 Remove Active Entries...................................................................................................................................... 37 Deactivate All Entries ....................................................................................................................................... 37 The Select Menu.................................................................................................................................................... 38 Feature Selector ... ............................................................................................................................................. 38 All ...................................................................................................................................................................... 39 All Bases ........................................................................................................................................................... 39 Select All Features in Non-matching Regions .................................................................................................. 39 None .................................................................................................................................................................. 40 By Key............................................................................................................................................................... 40 CDS Features..................................................................................................................................................... 40 Same Key .......................................................................................................................................................... 40 Open Reading Frame ......................................................................................................................................... 40 Features Overlapping Selection ........................................................................................................................ 40 Features Within Selection ................................................................................................................................. 41 Base Range ... .................................................................................................................................................... 41 Feature AA Range ... ......................................................................................................................................... 41 Toggle Selection ................................................................................................................................................ 41 The View Menu ..................................................................................................................................................... 41 Selected Features ............................................................................................................................................... 41 Selection ............................................................................................................................................................ 41 Search Results ................................................................................................................................................... 42 CDS Genes And Products ................................................................................................................................. 42 Feature Filters .................................................................................................................................................... 42 Suspicious Start Codons ... ............................................................................................................................ 42 Suspicious Stop Codons ... ............................................................................................................................ 43 Non EMBL Keys ... ....................................................................................................................................... 43 Duplicated Features ... ................................................................................................................................... 43 Overlapping CDS Features ........................................................................................................................... 43 Features Missing Required Qualifiers ... ....................................................................................................... 43 Filter By Key ... ............................................................................................................................................. 43 Selected Features ... ....................................................................................................................................... 43 Overview ........................................................................................................................................................... 43 Sequence Statistics ........................................................................................................................................ 44 Feature Statistics ........................................................................................................................................... 44 Forward Strand Overview ................................................................................................................................. 45 Reverse Strand Overview .................................................................................................................................. 45 Feature Bases..................................................................................................................................................... 45 Feature Bases As FASTA ................................................................................................................................. 45 Feature Amino Acids As FASTA ..................................................................................................................... 45 Feature Statistics ............................................................................................................................................... 45 Feature Plots ...................................................................................................................................................... 45 The Goto Menu ..................................................................................................................................................... 46 Navigator ... ....................................................................................................................................................... 46 Start of Selection ............................................................................................................................................... 47 End of Selection ................................................................................................................................................ 47 Feature Start ...................................................................................................................................................... 47 Feature End ....................................................................................................................................................... 48 Start of Sequence ............................................................................................................................................... 48 End of Sequence ................................................................................................................................................ 48 Feature Base Position ... .................................................................................................................................... 48 Feature Amino Acid ... ...................................................................................................................................... 48 The Edit Menu ....................................................................................................................................................... 48 Undo .................................................................................................................................................................. 48 Redo .................................................................................................................................................................. 49 Selected Features in Editor ................................................................................................................................ 49 Subsequence (and Features) .............................................................................................................................. 51 Find Or Replace Qualifier Text ......................................................................................................................... 51 Qualifier(s) of Selected Feature ........................................................................................................................ 52 Change ... ....................................................................................................................................................... 52 Remove ......................................................................................................................................................... 52 Convert ... ...................................................................................................................................................... 52 Selected Feature(s) ............................................................................................................................................ 52 Duplicate ....................................................................................................................................................... 52 Merge ............................................................................................................................................................ 52 Unmerge ........................................................................................................................................................ 53 Unmerge All Segments ................................................................................................................................. 53 Delete ............................................................................................................................................................ 53 Delete Exons ................................................................................................................................................. 53 Remove Introns ............................................................................................................................................. 53 Move Selected Features To ............................................................................................................................... 53 Copy Selected Features To ................................................................................................................................ 53 Trim Selected Features ...................................................................................................................................... 54 To Met ........................................................................................................................................................... 54 To Any........................................................................................................................................................... 54 To Next Met .................................................................................................................................................. 54 To Next Any .................................................................................................................................................. 54 Extend Selected Features .................................................................................................................................. 54 To Previous Stop Codon ............................................................................................................................... 54 To Next Stop Codon ...................................................................................................................................... 55 To Next Stop Codon and Fix......................................................................................................................... 55 Fix Stop Codons ................................................................................................................................................ 55 Automatically Create Gene Names ................................................................................................................... 55 Fix Gene Names ................................................................................................................................................ 55 Bases.................................................................................................................................................................. 55 Reverse And Complement ............................................................................................................................ 55 Reverse And Complement Selected Contig .................................................................................................. 56 Delete Selected Bases.................................................................................................................................... 56 Add Bases At Selection ................................................................................................................................. 56 Add Bases From File ... ................................................................................................................................. 56 Replace Bases At Selection ........................................................................................................................... 56 Contig Reordering ... ......................................................................................................................................... 56 Header Of Default Entry ................................................................................................................................... 57 The Create Menu ................................................................................................................................................... 57 New Feature ...................................................................................................................................................... 57 Feature From Base Range ................................................................................................................................. 57 Intergenic Features ............................................................................................................................................ 57 Features From Non-matching Regions ............................................................................................................. 57 New Entry ......................................................................................................................................................... 58 Mark Open Reading Frames ... ......................................................................................................................... 58 Mark Empty ORFs ... ........................................................................................................................................ 58 Mark Open Reading Frames In Range ... .......................................................................................................... 58 Mark From Pattern ... ........................................................................................................................................ 58 Mark Ambiguities ............................................................................................................................................. 59 The Run Menu ....................................................................................................................................................... 59 Configuring the Run Menu ............................................................................................................................... 59 Searching and Using Local Sequence Databases for Mac OSX ....................................................................... 60 The Graph Menu ................................................................................................................................................... 61 Hide All Graphs ................................................................................................................................................ 61 Add Usage Plots ... ............................................................................................................................................ 62 Add User Plot ... ................................................................................................................................................ 62 GC Content (%) ................................................................................................................................................. 64 GC Content (%) With 2.5 SD Cutoff ................................................................................................................ 64 AG Content (%) ................................................................................................................................................ 64 GC Frame Plot ................................................................................................................................................... 65 Correlation Scores ............................................................................................................................................. 65 Reverse Correlation Scores ............................................................................................................................... 65 GC Deviation (G-C)/(G+C) .............................................................................................................................. 65 AT Deviation (A-T)/(A+T) ............................................................................................................................... 65 Karlin Signature Difference .............................................................................................................................. 66 Cumulative AT Skew and Cumulative GC Skew ............................................................................................. 66 Positional Asymmetry ....................................................................................................................................... 66 Informational Entropy ....................................................................................................................................... 66 Scaled Chi Square ............................................................................................................................................. 66 Mutational Response Index ............................................................................................................................... 66 Effective Codon Number .................................................................................................................................. 67 Intrinsic Codon Deviation Index ....................................................................................................................... 67 The Display Menu ................................................................................................................................................. 67 Show Entry Buttons .......................................................................................................................................... 67 Show Base View ............................................................................................................................................... 67 Show Feature List.............................................................................................................................................. 67 The Entry Button Line........................................................................................................................................... 68 The Overview and DNA Views ............................................................................................................................ 68 Changing the Selection from a View Window .................................................................................................. 68 Other Mouse Controlled Functions ................................................................................................................... 69 The Pop-up Menu .............................................................................................................................................. 69 Pop-up Menu Functions ................................................................................................................................ 69 Toggle Buttons .............................................................................................................................................. 70 Scrolling The View ........................................................................................................................................... 71 Changing The Scale .......................................................................................................................................... 71 "Direct Editing" ................................................................................................................................................. 72 The Feature List .................................................................................................................................................... 72 Changing the Selection from the Feature List ................................................................................................... 72 Other Mouse Controlled Functions ................................................................................................................... 72 The Pop-up Menu .............................................................................................................................................. 73 Save List to File............................................................................................................................................. 73 Show Selected Qualifier ................................................................................................................................ 73 Show Correlation Scores ............................................................................................................................... 73 Show Gene Names ........................................................................................................................................ 73 Show Qualifiers ............................................................................................................................................. 73 Show Product ................................................................................................................................................ 73 Scrolling The List .............................................................................................................................................. 74 Graphs and Plots.................................................................................................................................................... 74 Annotation Validation ........................................................................................................................................... 74 How to Run Validation Checks ......................................................................................................................... 74 Validation Checks For All File Types............................................................................................................... 75 Validation Checks For GFF3 ............................................................................................................................ 75 Validation Report .............................................................................................................................................. 76 Notes on Using The Mouse ................................................................................................................................... 76 Chapter 4. Project File Manager ........................................................................................................................... 78 Overview ............................................................................................................................................................... 78 Using the Project File Manager ............................................................................................................................. 78 Chapter 5. Secure Shell (SSH) Plugin To Artemis ............................................................................................... 80 Overview of the SSH Plugin ................................................................................................................................. 80 Login In ................................................................................................................................................................. 80 Setting up a SSH tunnel ........................................................................................................................................ 81 Using Putty to Set Up A Tunnel............................................................................................................................ 85 Chapter 6. Artemis Configuration Options .......................................................................................................... 92 The Options File .................................................................................................................................................... 92 Artemis Option Descriptions ................................................................................................................................. 92 font_size ............................................................................................................................................................ 92 font_name .......................................................................................................................................................... 92 base_plot_height................................................................................................................................................ 93 feature_plot_height............................................................................................................................................ 93 draw_feature_borders ........................................................................................................................................ 93 show_forward_lines .......................................................................................................................................... 93 show_reverse_lines ........................................................................................................................................... 93 draw_feature_arrows ......................................................................................................................................... 93 overview_feature_labels .................................................................................................................................... 94 overview_one_line_per_entry ........................................................................................................................... 94 show_list............................................................................................................................................................ 94 show_base_view................................................................................................................................................ 94 features_on_frame_lines ................................................................................................................................... 94 frame_line_features ........................................................................................................................................... 94 feature_labels .................................................................................................................................................... 94 one_line_per_entry ............................................................................................................................................ 95 genetic_codes .................................................................................................................................................... 95 translation_table_1 ............................................................................................................................................ 95 extra_keys.......................................................................................................................................................... 96 extra_qualifiers .................................................................................................................................................. 96 common_keys.................................................................................................................................................... 96 hyperlinks .......................................................................................................................................................... 96 undo_levels........................................................................................................................................................ 96 minimum_orf_size ............................................................................................................................................ 97 direct_edit .......................................................................................................................................................... 97 feature_dna_programs ....................................................................................................................................... 97 feature_protein_programs ................................................................................................................................. 97 ncbi_dna_search ................................................................................................................................................ 97 ncbi_protein_search .......................................................................................................................................... 97 Setting Colours .................................................................................................................................................. 98 Options For Plots and Graphs ........................................................................................................................... 98 Options For A Chado Database ......................................................................................................................... 99 chado_exon_model........................................................................................................................................ 99 chado_transcript ............................................................................................................................................ 99 chado_servers ................................................................................................................................................ 99 Options File Format .............................................................................................................................................. 99 An Example Options File ................................................................................................................................ 100 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.