options

# The standard options file for Artemis

# (Note that comment lines start with a hash (#) symbol)

# $Header: //tmp/pathsoft/artemis/etc/options,v 1.32 2007-09-11 10:59:05 tjc Exp $

# 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 = 12


# Set the name of the font to use in Artemis.  These possibilites are
# available on all platforms:
#   Dialog, DialogInput, Monospaced, Serif, SansSerif, Symbol.

font_name = Monospaced

# This option is used to set the default minimum size (in amino acids)
# of a "large" open reading frame, which controls which ORFS are
# marked by the "Mark Open Reading Frames" menu item.

minimum_orf_size = 100

# Set the default value for the direct edit option (see
# http://www.sanger.ac.uk/Software/Artemis/stable/manual/launch-window.html#LAUNCH-WINDOW-OPTIONS-DIRECT-EDIT
# for more)
direct_edit = yes

# This setting controls which set of codons will be used for start codons.
# This can be changed from the options menu.
# Give the translation table number.
#
genetic_code_default = 1

# This option gives the bases of the possible start codons
eukaryotic_start_codons = atg
prokaryotic_start_codons = atg gtg ttg


#
# Genetic Codes :
# http://www3.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
# http://www.ncbi.nlm.nih.gov/collab/FT/#7.5.5
#

genetic_codes = \
     Standard \
     Vertebrate_Mitochondrial \
     Yeast_Mitochondrial \
     Mold,_Protozoan,_Coelenterate_Mitochondrial_and_Mycoplasma/Spiroplasma \
     Invertebrate_Mitochondrial \
     Ciliate_Dasycladacean_and_Hexamita \
     - \
     - \
     Echinoderm_Flatworm_Mitochondrial \
     Euplotid \
     Bacterial_and_Plant_Plastid \
     Alternative_Yeast_Nuclear \
     Ascidian_Mitochondrial \
     Alternative_Flatworm_Mitochondrial \
     Blepharisma_Nuclear \
     Chlorophycean_Mitochondrial \
     - \
     - \
     - \
     - \
     Trematode_Mitochondrial \
     Scenedesmus_Obliquus_Mitochondrial \
     Thraustochytrium_Mitochondrial

# 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, ...,
#   ...

# 1. standard code (default)
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

start_codons_1 = atg

#
# For the following Genetic Code tables the differences
# from the Standard Code are given.
#
#
# 2. Vertebrate Mitochondrial Code
#
translation_table_2 = \
      aga* agg* atam tgaw
 
start_codons_2 = atg      
#start_codons_2_bos = ata
#start_codons_2_homo = ata att
#start_codons_2_mus = ata att atc
#start_codons_2_coturnix_gallus = gtg 

# 3. Yeast Mitochondrial Code
translation_table_3 = \
      atam cttt ctct ctat ctgt tgaw

start_codons_3 = ata atg

# 4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the
#    Mycoplasma/Spiroplasma Code 
translation_table_4 = \
      tgaw

start_codons_4 = atg

#start_codons_4_Trypanosoma = tta ttg ctg
#start_codons_4_Leishmania = att ata
#start_codons_4_Tertrahymena = att ata atg
#start_codons_4_Paramecium = att ata atg atc gtg gta

# 5. Invertebrate Mitochondrial Code
translation_table_5 = \
      agas aggs atam tgaw

start_codons_5 = atg ata att
#start_codons_5_apis = atg ata atc att
#start_codons_5_polyplacophora = atg ata gtg

# 6. Ciliate, Dasycladacean and Hexamita Nuclear Code
translation_table_6 = \
      taaq tagq 

start_codons_6 = atg

# 9. Echinoderm and Flatworm Mitochondrial Code
translation_table_9 = \
      aaan agas aggs tgaw 

start_codons_9 = atg gtg

# 10. Euplotid Nuclear Code
translation_table_10 = \
      tgac

start_codons_10 = atg

# 11. Bacterial and Plant Plastid 
translation_table_11 = 

start_codons_11 = atg gtg ttg

# 12. Alternative Yeast Nuclear Code
translation_table_12 = \
      ctgs

start_codons_12 = ctg atg

# 13.  Ascidian Mitochondrial Code      
translation_table_13 = \
      agag aggg atam tgaw
 
start_codons_13 = atg

# 14. Alternative Flatworm Mitochondrial Code
translation_table_14 = \
      aaan agas aggs taay tgaw

start_codons_14 = atg

# 15. Blepharisma
translation_table_15 = \
      tagq

start_codons_15 = atg

# 16. Chlorophycean Mitochondrial
translation_table_16 = \
      tagl

start_codons_16 = atg

# 21. Trematode Mitochondrial
translation_table_21 = \
      tgaw atam aaan agas aggs

start_codons_21 = atg gtg

# 22. Scenedesmus obliquus mitochondrial
translation_table_22 = \
      tca* tagl

start_codons_22 = atg

# 23. Thraustochytrium Mitochondrial 
translation_table_23 = \
      tta*

start_codons_23 = att atg gtg

# 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 = 245 245 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

# GeneDB colours
#
colour_101 = 102 51 153
colour_102 = 153 102 204
colour_103 = 255 248 220

#
#

colour_of_CDS = 5
colour_of_cds? = 7
colour_of_BLASTCDS = 2
colour_of_BLASTN_HIT = 6
colour_of_CRUNCH_D = 2
colour_of_CRUNCH_X = 15
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_exon = 7
colour_of_mRNA = 1
colour_of_tRNA = 8
colour_of_TATA = 3
colour_of_bldA = 2
colour_of_GFF = 11

colour_of_start_codon = 6

# suffixes used on files that contain features - used in file requesters
feature_file_suffixes = tab embl gbk genbank tab_embl gff feature feat \
   art artemis

# suffixes used on files that contain sequence - used in file requesters
sequence_file_suffixes = embl gbk genbank gff tab_embl seq dna \
   art artemis

# 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


# the default height for the base plot window
base_plot_height = 150


# the default height for the feature plot window
feature_plot_height = 160


# if this option is no then the feature labels in the overview will be off at
# startup (the default is yes)
# overview_feature_labels = no


# if this option is yes then the overview will start in one line per entry
# mode (the default is no)
# overview_one_line_per_entry = yes


# if this option is "yes" then the feature list will be displayed on startup
# (this is the default)
show_list = yes


# if this option is "yes" then the base view will be displayed on startup
# (this is the default)
show_base_view = yes


# if this option is "yes" then the entry buttons will be displayed on
# startup
show_entry_buttons = yes


# if this option is "yes" then artemis will offer to show the results of a
# search when it finishes
show_results = no


# if this option is "yes" the "all features on frame lines" option will
# default to true on start up
features_on_frame_lines = no


# if this option is "yes" the "feature labels" option will
# default to true on start up
feature_labels = yes


# if this option is "yes" the "one line per entry" option will default to
# true on start up 
one_line_per_entry = no


# 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


# 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.
draw_feature_borders = 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.
draw_feature_arrows = yes


# the number of levels of undo to save or 0 if undo is disabled.  more undo
# levels will require more memory.
undo_levels = 20


# this list is added to the keys from the feature_keys file
extra_keys = \
    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 CRUNCH_X fasta_record allele mutation splicesite \
    TMM signalP

# this list is added to the keys from the feature_keys_gff file
extra_keys_gff =

# Names of qualifiers to search when attempting to find the primary or display
# name of a gene.  These qualifiers names are searched in order when looking
# for gene names.
display_name_qualifiers = primary_name synonym systematic_id \
    temporary_systematic_id gene locus_tag label Name ID

# Names of qualifiers to search when attempting to find the systematic name of
# a gene
systematic_name_qualifiers = systematic_id temporary_systematic_id \
     locus_tag gene label Name ID


# this list is added to the qualifiers from the qualifier_types file
extra_qualifiers = \
    CHROMO_LINK text \
    C_processing "text" \
    C_processing_BigPi "text" \
    C_processing_DGPI "text" \
    COM_NAME "text" \
    FEAT_NAME text \
    GO_component "text" \
    GO_function "text" \
    GO_process "text" \
    GO_slim "text" \
    GO "text" \
    LOCUS "text"  \
    PUB_LOCUS text \
    PUB_COMMENT "text" \
    REPEAT_TYPE "text" \
    SNP "text" \
    algorithm "text" \
    anchor "text" \
    annotation_source "text" \
    assembly_id "text" \
    bb_orthologue "text" \
    bound_moiety "text" \
    bpp_orthologue "text" \
    bp_orthologue "text" \
    bicsw_file "text" \
    blast_score text \
    blast_file "text" \
    blastn_file "text" \
    blastp_file "text" \
    blastp+go_file "text" \
    blastp_match "text" \
    blastx_file "text" \
    cds_id "text" \
    chloroplast "text" \
    chromoplast "text" \
    class "text" \
    cleavage "text" \
    cluster "text" \
    color text \
    colour text \
    comment_Cterm "text" \
    comment_Nterm "text" \
    confidence_level "text" \
    controlled_curation "text" \
    coord "text" \
    contig_id "text" \
    created "text" \
    curation "text" \
    curated_ortholog "text" \
    cyanelle "text" \
    domain "text" \
    end_phase text \
    exon_id "text" \
    fasta_file "text" \
    fasta_match "text" \
    fastx_file "text" \
    filename "text" \
    function "text" \
    gene "text" \
    gene_id "text" \
    gff_feature text \
    gff_group text \
    gff_seqname text \
    gff_source text \
    go_from_interpro "text" \
    hp_match "text" \
    hth_file "text" \
    id "text" \
    interaction "text" \
    interpro "text" \
    job "text" \
    label text \
    literature "text" \
    manual none \
    mitochondrion "text" \
    modified "text" \
    mutation "text" \
    note "text" \
    obsolete_name "text" \
    obsolete_product "text" \
    origid "text" \
    ortholog "text" \
    other_transcript  "text" \
    paralog "text" \
    pepstats_file "text" \
    percent_id text \
    pfam_match "text" \
    previous_other_transcript "text" \
    previous_shared_id "text" \
    previous_systematic_id "text" \
    primary_name "text" \
    prosite_match "text" \
    psu_db_xref "text" \
    psu_domain "text" \
    reserved_name "text" \
    query_id text \
    score text \
    sequence_source "text" \
    sequence_status "text" \
    shared_id "text" \
    sigcleave_file "text" \
    signal "text" \
    similarity "text" \
    smart_file "text" \
    sptr_display "text" \
    start_phase text \
    subject_end text \
    subject_id text \
    subject_start text \
    synonym "text" \
    synteny "text" \
    systematic_id "text" \
    taxon_id "text" \
    tblastn_file "text" \
    tblastx_file "text" \
    tb_orthologue "text" \
    temporary_systematic_id "text" \
    tmhelix "text" \
    transferred_gene "text" \
    transferred_locus_tag "text" \
    transferred_note "text" \
    transferred_primary_name "text" \
    transferred_product "text" \
    transferred_synonym "text" \
    transferred_systematic_id "text" \
    type "text"

# this list is added to the qualifiers from the qualifier_types_gff file
extra_qualifiers_gff = \
    blast_score text \
    blast_file "text" \
    blastn_file "text" \
    blastp_file "text" \
    blastp+go_file "text" \
    blastx_file "text" \
    cluster "text" \
    controlled_curation "text" \
    fasta_file "text" \
    GO "text" \
    note "text" \
    orthologous_to "text" \
    paralogous_to "text" \
    similarity "text"

# this is a list of extra qualifiers that are legal but are not displayed in
# popup menus (such as the one in the feature editor window).  this hack is
# used by diana.components.QualifierChoice to limit the number of qualifers
# that are displayed in the popup menu.  on some VMs if there are too many in
# the popup the bottom ones aren't visible
invisible_qualifiers = \
    CHROMO_LINK    \
    C_processing       \
    C_processing_BigPi \
    C_processing_DGPI  \
    COM_NAME       \
    FEAT_NAME      \
    LOCUS          \
    PUB_LOCUS      \
    PUB_COMMENT    \
    REPEAT_TYPE    \
    SNP            \
    bicsw_file     \
    blast_file     \
    blast_score    \
    blastn_file    \
    blastp+go_file \
    blastp_file    \
    blastx_file    \
    cds_id         \
    chloroplast    \
    chromoplast    \
    codon          \
    comment_Cterm  \
    comment_Nterm  \
    created        \
    cyanelle       \
    end_phase      \
    exception      \
    exon_id        \
    fasta_file     \
    fasta_match    \
    gene_id        \
    go_from_interpro \
    hp_match       \
    hth_file       \
    interpro       \
    map            \
    mitochondrion  \
    modified       \
    number         \
    obsolete_gene_name \
    pepstats_file  \
    percent_id     \
    pfam_match     \
    prosite_match  \
    psu_domain     \
    reserved_gene_name \
    query_id       \
    sigcleave_file \
    score          \
    smart_file     \
    start_phase    \
    tblastn_file   \
    tblastx_file   \
    temporary_systematic_id \
    transl_table   \
    translation    \
    type           \
    usedin

invisible_qualifiers_gff= \
    class          \
    cluster        \
    controlled_curation \
    Derives_from   \
    feature_id     \
    feature_relationship_rank \
    gff_feature    \
    gff_group      \
    gff_seqname    \
    gff_source     \
    GO             \
    ID             \
    Name           \
    note           \
    Ontology_term  \
    orthologous_to \
    paralogous_to  \
    Parent         \
    product        \
    similarity     \
    Target         \
    timelastmodified  


# These pairs consist of a program name and a parameter string.
# For blast and fasta the parameter string is the name of the database to
# search.
#
# /nfs/pathsoft/databases/GO/new
# /nfs/pathsoft/databases/protein/go_all
feature_protein_programs = \
    fasta %uniprot \
    fasta %uniprot_archaea \
    fasta %uniprot_bacteria \
    fasta %uniprot_eukaryota \
    fasta %uniprot_viruses \
    fasta %uniprot_rest \
    fasta %malaria \
    fasta %kineto_aa \
    sigcleave 0 \
    pepstats - \
    blastp %uniprot \
    blastp %uniprot_archaea \
    blastp %uniprot_bacteria \
    blastp %uniprot_eukaryota \
    blastp %uniprot_viruses \
    blastp %uniprot_rest \
    blastp psu/Kineto_aa \
    tblastn %embl_other \
    blastp+go psu/go_all \
    blastp+go /nfs/pathsoft/databases/GO/new/go_all \
    hth - \
    smart - \
    clustalx PROTEIN \
    jalview PROTEIN

feature_dna_programs = \
    tblastx %embl_other \
    blastn %embl_other \
    blastx %uniprot \
    fastx %uniprot \
    clustalx DNA

application_programs = \
    jalview

mess_fasta_hits = 10

# 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 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 BLASTCDS 3'UTR 5'UTR

#srs_url = http://srs.sanger.ac.uk/srsbin/cgi-bin/ 
srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
pubmed_url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=