How to use Artemis to view DNannotator's output standard Genbank format

 

can be obtained from Sanger Center

1. Input:

    1) FASTA format sequence data or standard Genbank format sequence with both "gb-header" and sequence body. 

   If you prefer to have a complete Genbank format data file with sequence in, you can use function (Format Genbank format sequence) to create Genbank data. BUT, THIS IS NOT NECCESSARY.

   Artemis can take FASTA format sequence data and gb-header files separately.

    2) gb-header files generated by DNannotator with new annotation included.

    BUT, Exon analysis results may contain some warning messages which are not recognizable for Artemis.

    Clean gb-header function can help you to remove those warning messages.

2. After installation as specified by Artemis manual.

Start Artemis with command as (certainly you will need to have Java installed in your machine), go to the directory contains files "Diana.java" and "Diana.class", (assuming you have only limited amount of computer memory), key in command of:

    java -jar -Xmx512m Diana

    Then, Artemis will start.

3. In menu bar, File -> Open,  read in either FASTA format sequence data or Genbank format data with sequence (currently, Artemis has problem reading NCBI's gDNA assembly in Genbank format for "CONTIG" data.  So, you may use FASTA format one);

    File -> Read An Entry, read in gb-header files (without sequence, but should be gb-header for sequence above.)

    Read in other input files as listed in (1).

    There are three panels showing up.  Upper panel is for graphic icons of all annotation elements; middle panel is for sequence; lower panel is for list of all features.

4.  Right click in upper panel area (command + button in Mac OS), in the pop-up menu,

check all following items:

 Then, each entry will have its own annotation line up horizontally in one track in upper panel.  Annotation from different entries line up vertically in upper panel.

Check or uncheck the box for each entry will hide or show corresponding entry's data.

5. If you don't want to six-frame translation in middle panel, right-click in middle panel, in the pop-up menu,

uncheck both "Forward" and "Reverse frame lines".

6. To view the whole region, Menu -> Select -> Base Range, input the whole range coordinates.

    for example, if the sequence is 16 Mbp, put in "1..16000000" (don't over the limit.)

    Then, the whole sequence is selected.

    In upper panel area, right-click, -> Zoom to Selection

    Here you can obtain the view as captured here.

    (click for large view)

7. If you want to add additional layer for GC%

    Menu -> Display -> GC %

    Here is the view you can get.

(click for large view)

8. The scroll bar at the right of upper and middle panels are designed for "zoom in/out" the view. But if your data file is big, such as more than 10 Mb, don't try that.  It can freeze your window.

    Select -> base range, then, Zoom to Selection as described in 6. is the best choice to Zoom in/out.

(click for large view)

9. The highlighted feature and sequence are shaded in yellow. Contents in three different panels are internally related.  Clicking on one of the features can bring you to the sequence, and its icon.

10. Many more functions to play with.  Here I can only give you a easy start point, to avoid those traps I had ever been in.

    Zoom in/out is the most troublesome part.  Finding the way to hide/show annotation layers is also tricky, at least for me.