Getting and Installing Release 5

• FTP: Artemis V5 for Unix and GNU/Linux WWW: Artemis V5 for Unix and GNU/Linux
• FTP: Artemis V5 for Macintosh WWW: Artemis V5 for Macintosh
• FTP: Artemis V5 for Windows WWW: Artemis V5 for Windows

Once downloaded on a Macintosh or Windows machine, the compiled versions are ready to run (assuming you have the appropriate version of Java installed). Unix users will need to unpack the archive first (see the manual for details).

Full installation instructions are in the v5 user manual. The manual is also available as one big file. Further information on installation or other matters relating to the program can be obtained from Kim Rutherford (kmr@sanger.ac.uk).

Changes

Changes in Release 5 (??? 2003)

• Artemis now has an undo facility which will undo up to 20 feature or entry changes. [details...]
• Artemis can now read the output of blastall version 2.2.2 when blastall is run with the -m 8 flag. [details...]
• There are now no warning about non-standard qualifiers when reading flatfiles in EMBL format generated from Ensembl.
• Added "Karlin Signature Difference" graph. [details...]
• A Graph menu has been added which contains the graph/plot controls that were in the Display menu.
• When searching for amino acid strings using the feature navigator, the letter X is now treated as an ambiguity code.
• Added "Goto Feature With Gene Name:" to the feature navigator. [details...].
• Added an "Ignore Case" toggle button to the navigator window.
• Added "Flip Display" to the popup menu. [details...].
• Speed improvements for people who use lots of sequence features (where "lots" means thousands or more). In particular, deleting features and removing entries should be much faster.
• Added an option that allows the active entry to be highlighted when "One Line Per Entry" is on. [details...]
• Added a toggle for switching between eukaryotic and prokaryotic mode. [details...]
• When viewing or writing amino acid sequences in prokaryotic mode the first codon will always be translated as a methionine even if the normal translation is a valine or leucine.
• A temporary feature is now created for each record in a FASTA database so that FASTA files can be viewed more easily. The features are read-only and aren't saved if the FASTA file is saved.
• The overview window has been rearranged to make things more clear. [details...]
• The selection viewer now shows the average/min/max correlation score and GC content of the selected features. [details...]
• Removed the extra blank lines that were being inserted between the header lines of GENBANK entries when saving.
• Added the run_pepstats script and a menu item to the Run menu for running pepstats.
• Added three new buttons to the feature editor: "Remove Range", "Select Feature" and "Goto Feature". [details...]
• The main Artemis window should now be smaller the screen size, even on laptops with small displays.
• Fixed a bug that made selected items in the feature list hard to read on Windows machines.
• Fixed GFF reading and writing to correctly handle the frame field, so GFF features should now be in the correct frame. The GFF reading code should now be GFF2 compatible.
• The search scripts that can generate large amounts of output (run_fasta, run_blastp etc.) now compress the output with gzip.
• The Feature Selector has two new buttons:
  • "Allow Partial Match"
  • "Amino Acid Motif"
• Fixed "Trim to Met" to cope with features that have a /codon_start qualifier.
• The complement of base 'X' is now 'X'.
• "Mark Open Reading Frames ..." and "Select"->"Open Reading Frame" now treat any codon that contains an 'X' as a stop codon. All other non-translatable codons are still treated as non-stop codons.
• Font fixes for UNIX and GNU/Linux systems running Java 2.
• Added some new option settings:
  • font_name [details...]
  • draw_feature_borders [details...]
  • draw_feature_arrows [details...]
  • show_base_view [details...]
  • features_on_frame_lines [details...]
  • one_line_per_entry [details...]
  • feature_labels [details...]
• Changed run_blastn, run_blastp etc. to use blast2 (blastall_2.0.11 to be exact). The release 4 scripts will work with release 5.
• The run scripts have been moved to the etc directory so that they can be shared with ACT.
• "Read Features Into" has been renamed to "Read Entry Into" for consistency.
• New menu items:
  • "Change Qualifiers Of Selected ..." in the Edit menu. [details...]
  • "Remove Qualifier Of Selected ..." in the Edit menu. [details...]
  • "Unmerge Selected Feature" in the Edit menu which allows multi-exon features to be split up. [details...]
  • "Extend to Next Stop Codon" in the Edit menu will move the end of the feature to the codon just before the next stop codon. [details...]
  • "Extend to Previous Stop Codon" in the Edit menu will move the start of the feature to the codon just after the previous stop codon. [details...]
  • "Fix Gene Names" in the Edit menu. [details...]
  • "Add Bases From File ..." in the Edit menu. [details...]
  • A new menu item to toggle the display of arrows on features [details...]. and a new menu item to toggle the display of borders on features [details...].

Changes in Release 4 (November 2000)

• Artemis will now create an autosave file for each unsaved entry every time ten minutes. The names of the autosave files follow the emacs system - eg. for a file named features.tab the autosave file is called #features.tab#
• The "Search Results" menu item is now available again on non-UNIX systems. It was removed by mistake before the last release. [details...]
• Artemis can now read the output of MSPcrunch, when MSPcrunch is run with the -x or -d flags.
• Some problems with GFF file reading and writing have been fixed. The ability to save arbitrary features in GFF format has also been added.
• Mark start codons - colour can be changed in the options file.
• Added the "Grab Range" button to the feature editor. [details...]
• Configuration options are now also read from $HOME/.artemis_options on UNIX and an extra options file can be given on the command line with the -options flag. [details...]
• The options file in the current directory can now be called "options", "options.txt" or "options.text". This change was made to make it easier for Windows users create options files. [details...]
• Default window size, maximum window size and minimum window size for the graphs can now be specified in the options file. [details...]
• More documentation about how to run external programs [details...] and how to change options [details ...].
• Shortcut for "Show Feature Plots" is now Control-W, which is easier to reach than Control-P.
• PC and Mac versions are smaller now because the CORBA library is not included.
• Added "Save List To File ..." in the feature list.
• Added "dribble" file. Changes made to features are now written to a file named .dribble.entry_name, where the entry_name is the name of the file that the feature is in. The dribble file is intended to help recover data after crashes or mistakes.
• Added the run_jalview script which can be used to run clustalw and the Jalview alignment viewer on the results of FASTA searches from within Artemis. To use this script you will also need Eric Sonnhammer's efetch (or getz from SRS), emma from EMBOSS, clustalw and a probably some knowledge of Perl. Contact kmr@sanger.ac.uk for more details.
• Added a work around for a bug in the Java VM on OSF1 which causes random crashes.
• The overview window now also shows the GC percentage of non-ambiguous bases. [details...]
• Double clicking the mouse in a base graph (such as the GC content graph) will now scroll to that base. Bases can be selected by clicking and dragging on a graph.
• Artemis will now obey the EMBL/GENBANK /transl_except qualifier. This is used to represent translational read-through of TGA stop codons, as well as other cases where the translation of a codon does not follow the expected translation table. For more information see the EMBL feature table definition.
• Upgraded the JacORB CORBA library to version 1.2.1 (this should be an invisible change).
• Artemis should now be faster when there are thousands of features loaded.
• The 'X' base code is now treated as a synonym for 'N'.
• The sequence reading code will now accept '.' as a base letter.
• The actions in the write menu will now ask before overwriting a file.
• New menu items:
  • Added "Feature Selector ..." to the Select menu. [details...]
  • "Feature AA Range ..." in the Select menu. [details...]
  • "Show Forward Frames", "Show Reverse Frames" and "One Line Per Entry" added to the popup menu. [details...]
  • "Hide All Graphs" added to the Display menu. [details...]
  • "Mark Ambiguities" in the Create menu. [details...]
  • "Show Log Window" and "Hide Log Window" in the Options menu. [details...]

Changes in Release 3 (March 2000)

• Extra menu items:
  • "Deactivate All Entries"
  • "Mark Empty ORFs ..."
  • "Show Forward Strand Overview"
  • "Show Reverse Strand Overview"
• The method for calling external programs on UNIX has changed slightly. Anyone with customized copies of run_fasta, run_blastp or the other scripts will need to remove line 8 (the one that mentions "DIANA_ENVIRONMENT_FILE").
• "Add Bases At Selection" and "Delete Selected Bases" have returned and now work well.

Changes in Release 2 (November 1999)

• Artemis can now read and write Genbank and GFF files.
• Extra menu items:
  • "Save Entry As/EMBL Format"
  • "Save Entry As/Genbank Format"
  • "Remove An Entry"
  • "Select Features in Range"
  • "Show CDS Genes And Products"
  • "View Feature Bases As FASTA"
  • "View Feature Amino Acids As FASTA"
  • "Edit Header Of Default Entry"
  • "Delete Selected Exons"
  • "Trim Selected Features To Next Met"
  • "Trim Selected Features To Next Any"
  • "Show Entry Buttons"
  • "Add Usage Plots ..."
  • "GC Content (%) With 2.5 SD Cutoff"
• Extra sub-menus:
  • "Feature Filters"
• "Save An Entry As EMBL ..." has changed to "Save Entry As/EMBL Submission Format"
• "Goto ..." has changed to "Navigator ..."
• The arguments to the external search scripts (run_blast, run_fasta, etc.) have changed: the -f argument is no longer necessary
• run_blast has been copied to run_blastp, to be more consistent with the other scripts (run_blast still exists)
• "Add Bases At Selection" and "Delete Selected Bases" in the Edit menu have been disabled, since they are currently unreliable. This will be fixed in the next release

Release 1 announced (August 1999)