This section describes the possible options for Artemis.
This option will set the font size for all the Artemis windows. The default font size is 14.
This option is used to set the minimum size 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).
This option gives the bases of the possible start codons.
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:
translation_table = \
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
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 Edit Selected Features 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 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 12 possible colours (numbered 0 to 12). 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 short names are documented in the section called The Display Menu in Chapter 3 and the section called Show 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