## This is "options.txt", the options file for Artemis (version 4), ## modified for display of features generated for the CardioGenomics ## sarcomere mutation database (www.cardiogenomics.org). ## ## Mostly, it defines particular keys (mutation, polymorphism, amplimer, ## primerF, primerR) and default colors for those keys. ## ## The original version of this document can be obtained from ## http://www.sanger.ac.uk/Software/Artemis/ ## ## Modified by Steve DePalma, 9/25/2001 # (Note that comment lines start with a hash (#) symbol) # This file should contain option settings that look like this: # # option_name = option_value # # If the value of an options is too long to fit on one line it can be split # over several lines by ending each line with a backslash like this: # # option_name = option_value another_option_value \ # a_third_option_value a_forth_option_value # This option will set the font size for all the Artemis windows. font_size = 14 draw_feature_arrows = no # This option is used to set the default minimum size of a "large" open # reading frame, which controls which ORFS are marked by the "Mark Open # Reading Frames" menu item. minimum_orf_size = 100 # This option gives the bases of the possible start codons start_codons = atg # This is the setting for S.coelicolor: # start_codons = atg gtg ttg # 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 table: # # 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 is the eukaryotic mitochondrial table: # # translation_table = \ # f f l l \ # s s s s \ # y y * * \ # c c w w \ # \ # l l l l \ # p p p p \ # h h q q \ # r r r r \ # \ # i i m m \ # t t t t \ # n n k k \ # s s * * \ # \ # v v v v \ # a a a a \ # d d e e \ # g g g g # the sequence of colour numbers must not have any gaps - if for example # colour_5 is missing then all colours with higher numbers will be ignored # the three numbers for each colour correspond to red, green and blue # respectively. each number is an intensity from 0 to 255 # white colour_0 = 255 255 255 # dark grey colour_1 = 100 100 100 # red colour_2 = 255 0 0 # green colour_3 = 0 255 0 # blue colour_4 = 0 0 255 # cyan colour_5 = 0 255 255 # magenta colour_6 = 255 0 255 # yellow colour_7 = 255 255 0 # pale green colour_8 = 152 251 152 # light sky blue colour_9 = 135 206 250 # orange colour_10 = 255 165 0 # brown colour_11 = 200 150 100 # pink colour_12 = 255 200 200 # light grey colour_13 = 170 170 170 # black colour_14 = 0 0 0 # reds: colour_15 = 255 63 63 colour_16 = 255 127 127 colour_17 = 255 191 191 ## CardioGenomics-specific colors colour_of_mutation = 2 colour_of_polymorphism = 12 colour_of_amplimer = 8 colour_of_primerF = 9 colour_of_primerR = 9 # colour_of_mRNA = 0 colour_of_CDS = 5 colour_of_exon = 7 colour_of_cds? = 7 colour_of_BLASTCDS = 2 colour_of_BLASTN_HIT = 6 colour_of_CRUNCH_D = 2 colour_of_source = 0 colour_of_prim_tran = 0 colour_of_stem_loop = 2 colour_of_misc_feature = 3 colour_of_misc_RNA = 12 colour_of_delta = 3 colour_of_LTR = 4 colour_of_repeat_region = 9 colour_of_repeat_unit = 9 colour_of_terminator = 3 colour_of_promoter = 3 colour_of_intron = 1 colour_of_tRNA = 8 colour_of_TATA = 3 colour_of_bldA = 2 colour_of_GFF = 11 colour_of_start_codon = 6 # this is the URL that contains the IOR of the EMBL server embl_ior_url = http://corba.ebi.ac.uk/EMBL/IOR/Embl.IOR # this is the URL that contains the IOR of the EnsEMBL server # ensembl_ior_url = file:///nfs/disk12/kmr/powmap/db.ior # if this option is "yes" the feature list will be displayed on startup (this # is the default) show_list = yes # if this option is "yes" Sanger specific menu items and functions will be # visible in the display sanger_options = no # the full path to the editor used for editing the qualifiers #external_editor = emacs # this list is added to the keys from the feature_keys file extra_keys = mutation polymorphism primerF primerR amplimer extra_keys = primerF primerR amplimer polymorphism \ BLASTN_HIT CDS_BEFORE CDS_AFTER CDS_before CDS_after \ CDS_motif BLASTCDS polymorphism GFF WUBLASTN_HIT \ WUBLASTX_HIT BLASTX_HIT TBLASTX_HIT BLASTN_HIT CRUNCH_D # this list is added to the qualifiers from the qualifier_types file extra_qualifiers = \ fasta_file "text" \ blast_file "text" \ blastx_file "text" \ blastn_file "text" \ blastp_file "text" \ tblastn_file "text" \ tblastx_file "text" \ bicsw_file "text" \ hth_file "text" \ sigcleave_file "text" \ label text \ colour text \ class "text" \ gene "text" \ gff_seqname text \ gff_feature text \ gff_source text \ gff_group text \ blast_score text \ subject_id text \ query_id text \ subject_start text \ subject_end text \ percent_id text \ score text \ hp_match "text" \ fasta_match "text" \ blastp_match "text" \ pfam_match "text" \ prosite_match "text" # These pairs consist of a program name and a parameter string feature_protein_programs = \ fasta %SNTU \ sigcleave 0 \ blast swir \ blastp swir \ tblastn embl_other \ hth - feature_dna_programs = \ tblastx embl_other \ blastn embl_other \ blastx swir application_programs = \ jalview # this is the list of keys that should be displayed by default in the edit # window common_keys = \ allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \ mutation polymorphism primerF primerR amplimer \ promoter source STS variation gene # 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