Changes in Release 11 (February 2009)

    * A print to PostScript option in Artemis and ACT has been added.
    * A NCBI search link has been added to the Run menu. This transfers the sequence automatically to the NCBI BLAST web page.
    * A new Find and Replace function for qualifier text has been added to the Edit menu. This has an option for boolean searches (e.g. and, or, &, |) of qualifier text. This includes an option to search for duplicate qualifiers.
    * Graph height can now be changed by simply dragging the divider at the bottom of the graphs.
    * DNAPlotter can be opened from the File menu for viewing the whole sequence as a circular or linear plot.
    * An option has been added to the graph plots popup menu to "Create features from graph peaks". This option appears for graphs plotting just one line. It creates features in regions above a given cut-off and above a given feature length.
    * An option has been added for writing Sequin table format.
    * New Convert Keys option has been added to convert keys of selected features (Edit->Qualifier(s) of Selected Feature->Convert ...).
    * When a file for a user plot is being selected an option has been added for taking the log transform of the user data.
    * Fix for creating intergenic features for overlapping CDS's. Also add note based on which one of the 4 cases with respect to the flanking CDS it belongs to, i.e.:
      IGR-F (forward): cds> IGR cds>
      IGR-R (reverse):
      IGR-B (both):
      IGR-X: cds> IGR
    * Use black_belt_mode to suppress warnings when opening Artemis.
    * On MacOSX - sequence files can be dragged and dropped on to the Artemis application to open sequences with file extensions: gff, embl, EMBL, genbank, gbk, fasta, seq, art and dna.

Database (Chado) changes

    * Added the ability to write sequence file formats (EMBL, GFF) from Artemis in database mode. With option to collapse the gene hierarchy (gene, transcript, exon) into a CDS feature.
    * A script (etc/writedb_entry) has been added to make it easier to write out multiple entries as EMBL / GFF files from chado. This uses Artemis read-write libraries and does not require each sequence to be launched from the database. For command line help run: etc/writedb_entry -help
    * Add java property option (-Dread_only) for read only databases.
    * An option in the database manager can be used to read feature data lazily from database. This can speed up reading from a large database and the opening of Artemis.
    * A list of available database servers can be defined in the options file.
    * Optimisation of reading from the database.