This section describes the possible options for Artemis.
This option will set the font size for all the Artemis windows. [default: 14]
This option is used to choose the font for all the Artemis windows. The font must be fixed-width. [default: "Monospaced"]
The height (in pixels) of each of the base plots. [default: 150]
The height (in pixels) of each of the feature plots. [default: 160]
If set to yes, borders will be drawn around each feature and each exon. if set to no, borders will only be drawn around the selected features. This can also be set in the views popup menu (see the section called Feature Borders in Chapter 3). [default: "yes"]
If set to yes, a direction arrow will be drawn around at the end of each feature. if set to no, no arrows will be drawn. This can also be set in the views popup menu (see the section called Feature Arrows in Chapter 3). [default: "yes"]
If this option is no then the feature labels in the overview (see the section called Overview of the Entry Edit Window in Chapter 3) will be off at startup. [default: "yes"]
If this option is set yes then the overview (see the section called Overview of the Entry Edit Window in Chapter 3) will start in one line per entry mode. [default: "no"]
If set to yes then the feature list (see the section called The Feature List in Chapter 3) will be shown on startup. [default: "yes"]
If set to yes then the DNA base view (see the section called The Overview and DNA Views in Chapter 3) will be shown on startup. [default: "yes"]
If set to yes then the "All Features On Frame Lines" option will be set to yes on startup. (See the section called All Features On Frame Lines in Chapter 3) [default: "no"]
This is a list of the feature keys that should be shown by default on the frame lines. e.g.
frame_line_features = \
CDS \
polypeptide
If set to yes then the feature labels will be shown on startup. (See the section called All Features On Frame Lines in Chapter 3) [default: "yes"]
If set to yes then the "One Line Per Entry" option will be set to yes on startup. (See the section called All Features On Frame Lines in Chapter 3) [default: "no"]
This option gives the list of names of the available genetic code tables. For each name in the list there is a translation_table_NUMBER entry (see below) where NUMBER is its location in the genetic_codes list. Similarly the start codons are defined as start_codons_NUMBER for each code.
The translation_table option is used to lookup codon translations. The table must have exactly 64 entries, and there is one entry for each codon.
The entries should appear in this order:
TTT TTC TTA TTG
TCT TCC ...
...
This is the default setting for this option is the Standard Code:
translation_table_1 = \
f f l l \
s s s s \
y y * * \
c c * w \
\
l l l l \
p p p p \
h h q q \
r r r r \
\
i i i m \
t t t t \
n n k k \
s s r r \
\
v v v v \
a a a a \
d d e e \
g g g g
The other translation table entries are defined by giving the differences to the Standard Code. These are given as the bases that make up the codon immediately followed by the translation (e.g. atam, so that 'ata' codes for 'm').
This contains a list of keys (separated by spaces) that are allowed in addition to those specified by EMBL. The official EMBL keys are listed in the feature_keys file in the Artemis code directory.
This contains a list of qualifiers (and their associated type) that are allowed in addition to those specified by EMBL. The official EMBL qualifiers and qualifier types are listed and described in the qualifier_types file in the Artemis code directory.
This is a list of the keys that should be shown by default in the feature edit window. (see the section called Selected Features in Editor in Chapter 3).
The default setting for this option is:
common_keys = \
allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \
mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \
repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \
tRNA unsure variation -10_signal -35_signal CDS_motif gene \
BLASTN_HIT CDS_BEFORE CDS_AFTER BLASTCDS
This is a list of databases and their URL's for Artemis to provide hyperlinks in the Feature Editor (see the section called Selected Features in Editor in Chapter 3).
The number of levels of undo to save or 0 to disable undo. More undo levels will require more memory. [default: 20]
This option is used to set the minimum size (in amino acid residues) of a "large" open reading frame, which controls which ORFS are marked by the "Mark Open Reading Frames" menu item (see the section called Mark Open Reading Frames ... in Chapter 3).
Set the default value for the direct edit option. A value of "yes" will turn direct edit on by default. See the section called Enable Direct Editing in Chapter 2
This is a list of the possible external programs that can be run on the bases of a feature. Each pair in the list is a program name and a default database to use for that program. For each program name there must be a corresponding shell script called "run_something". eg. run_blastn. See the section called Configuring the Run Menu in Chapter 3 for more information.
This is a list of the possible external programs that can be run on the translation of a feature. Each pair in the list is a program name and a default database to use for that program. For each program name there must be a corresponding shell script called "run_something". eg. run_blastp for blastp or run_fasta for fasta. See the section called Configuring the Run Menu in Chapter 3 for more information.
The feature colours (see the section called Feature Colours in Chapter 1) used by Artemis can be changed using the options file. By default there are 18 possible colours (numbered 0 to 17), but any number can be used. The option names for the colours are colour_0, colour_1, etc. The value of each of these qualifiers should be the three numbers separated by spaces. The numbers correspond to red, green and blue respectively and each number is an intensity from 0 to 255. As an example, to change colour 2 to white put this line in the options file:
colour_2 = 255 255 255
Here is a list of the default colour numbers:
0 white (RGB values: 255 255 255)
1 dark grey (RGB values: 100 100 100)
2 red (RGB values: 255 0 0)
3 green (RGB values: 0 255 0)
4 blue (RGB values: 0 0 255)
5 cyan (RGB values: 0 255 255)
6 magenta (RGB values: 255 0 255)
7 yellow (RGB values: 255 255 0)
8 pale green (RGB values: 152 251 152)
9 light sky blue (RGB values: 135 206 250)
10 orange (RGB values: 255 165 0)
11 brown (RGB values: 200 150 100)
12 pale pink (RGB values: 255 200 200)
13 light grey (RGB values: 170 170 170)
14 black (RGB values: 0 0 0)
15 mid red: (RGB values: 255 63 63)
16 light red (RGB values: 255 127 127)
17 pink (RGB values: 255 191 191)
Each graph type has three option settings associated with it: the default minimum window size, default maximum window size and the default window size. The option names have the following form: [short_name]_default_min_window, [short_name]_default_max_window and [short_name]_default_window (respectively). [short_name] should be replaced with the short name of the graph. (The available short names are documented in the section called The Graph Menu in Chapter 3 and the section called Feature Plots in Chapter 3).
As an example the short name of the GC content graph is gc_content so to set the initial minimum window size to 100, the maximum to 1000 and the initial window size to 150 use these setting:
gc_content_default_min_window = 100
gc_content_default_max_window = 1000
gc_content_default_window_size = 150