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    # The standard options file for Artemis
    
    # (Note that comment lines start with a hash (#) symbol)
    
    
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    # $Header: //tmp/pathsoft/artemis/etc/options,v 1.73 2009-08-06 16:15:19 tjc Exp $
    
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    # 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
    
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    # This option gives the bases of the possible start codons
    eukaryotic_start_codons = atg
    prokaryotic_start_codons = atg gtg ttg
    
    
    
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    #
    # Genetic Codes :
    
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    # http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
    
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    #
    
    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 \
    
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         Thraustochytrium_Mitochondrial \
         Pterobranchia_mitochondrial
    
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    # 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, ...,
    #   ...
    
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    # 1. standard code (default)
    translation_table_1 = \
    
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         F F L L \
         S S S S \
         Y Y # + \
         C C * W \
    
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                 \
    
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         L L L L \
         P P P P \
         H H Q Q \
         R R R R \
    
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                 \
    
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         I I I M \
         T T T T \
         N N K K \
         S S R R \
    
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                 \
    
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         V V V V \
         A A A A \
         D D E E \
         G G G G
    
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    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
    
    
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    start_codons_5 = ttg att atc ata atg gtg
    
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    #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
    
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    # 24. Pterobranchia mitochondrial
    translation_table_24 = \
          agas aggk tgaw
    
    start_codons_24 = ttg ctg atg gtg
    
    
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    # 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
    
    
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    # GeneDB colours
    #
    colour_101 = 102 51 153
    colour_102 = 153 102 204
    colour_103 = 255 248 220
    
    #
    #
    
    
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    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
    
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    sequence_file_suffixes = embl gbk genbank gff tab_embl seq dna \
    
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       art artemis fa fasta fas gb fna ffn
    
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    # this is the URL that contains the IOR of the EMBL server
    
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    #embl_ior_url = http://corba.ebi.ac.uk/EMBL/IOR/Embl.IOR
    
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    # 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
    
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    base_plot_height = 100
    
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    # 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 overview will start showing the feature
    # stack view (the default is no)
    # overview_feature_stack_view = yes
    
    
    
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    # 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 these options are "yes" the forward and reverse feature lines
    # are displayed
    show_forward_lines = yes
    show_reverse_lines = yes
    
    
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    # features to show on the frame line
    #frame_line_features =  \
    #  CDS \
    #  polypeptide
    
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    # 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
    
    
    # if yes then shortcut changed in Preferences are saved between sessions
    shortcut_cache = yes
    
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    # 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 = CDS uORF sORF tnaORF spliced_leader_RNA sequence_variant fasta_record
    
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    # 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.
    
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    display_name_qualifiers = primary_name Name synonym systematic_id \
        temporary_systematic_id gene locus_tag label ID
    
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    # Names of qualifiers to search when attempting to find the systematic name of
    # a gene
    systematic_name_qualifiers = systematic_id temporary_systematic_id \
    
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         locus_tag gene label ID Name
    
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    # this list is added to the qualifiers from the qualifier_types file
    extra_qualifiers = \
        CHROMO_LINK text \
    
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        C_processing "text" \
    
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        C_processing_BigPi "text" \
    
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        C_processing_DGPI "text" \
    
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        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" \
    
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        anchor "text" \
    
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        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" \
    
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        controlled_curation "text" \
    
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        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" \
    
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        note "text" \
    
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        obsolete_name "text" \
        obsolete_product "text" \
        origid "text" \
        ortholog "text" \
    
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        other_transcript  "text" \
    
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        paralog "text" \
        pepstats_file "text" \
        percent_id text \
        pfam_match "text" \
    
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        previous_other_transcript "text" \
        previous_shared_id "text" \
    
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        previous_systematic_id "text" \
        primary_name "text" \
        prosite_match "text" \
    
        pseudo none \
    
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        psu_db_xref "text" \
        psu_domain "text" \
        reserved_name "text" \
        query_id text \
        score text \
        sequence_source "text" \
        sequence_status "text" \
    
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        shared_id "text" \
    
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        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
    
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    extra_qualifiers_gff = \
    
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        blast_score text \
        blast_file "text" \
        blastn_file "text" \
        blastp_file "text" \
        blastp+go_file "text" \
        blastx_file "text" \
    
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        cluster "text" \
    
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        colour text \
        color text \
    
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        controlled_curation "text" \
        fasta_file "text" \
    
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        GO "text" \
    
        history "text" \
    
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        literature "text" \
    
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        note "text" \
    
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        orthologous_to "text" \
        paralogous_to "text" \
    
        polypeptide_domain "text" \
    
        previous_systematic_id "text" \
    
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        primary_name "text" \
    
        product_synonym "text" \
    
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        similarity "text" \
    
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        stop_codon_redefined_as_selenocysteine none \
    
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        synonym "text" \
    
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        systematic_id "text" \
        temporary_systematic_id "text"
    
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    # 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    \
    
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        C_processing       \
    
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        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  \
    
        pseudo         \
    
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        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
    
    
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    invisible_qualifiers_gff= \
    
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    	Alias          \
    
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    	allele         \
    	bound_moiety   \
    	cell_line      \
    	cell_type      \
    	charge         \
    	chromosome     \
    
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        class          \
    
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        clone          \
        clone_lib      \
    
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        cluster        \
    
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        controlled_curation \
    
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        country        \
        cultivar       \
    
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        cytoplasm_location \
    
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        cytoplasmic_polypeptide_region \
        Dbxref \
    
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        DNA_transposon \
    
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        Derives_from   \
    
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        dev_stage      \
        ecotype        \
        environmental_sample \
        estimated_length     \
        exception      \
    
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        feature_id     \
        feature_relationship_rank \
    
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        focus          \
    
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        Gap            \
    
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        gff_feature    \
        gff_group      \
        gff_seqname    \
        gff_source     \
        GO             \
    
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        GPI_anchored \
    
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        GPI_anchor_cleavage_site \
    
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        ID             \
    
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        insertion_seq  \
    
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        isObsolete \
    
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        isoelectric    \
        isolation_source \
        isolate        \
        kinetoplast    \
        lab_host       \
    
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        literature     \
    
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        locus_tag      \
        macronuclear   \
        map            \
        mass           \
    
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        membrane_structure \
    
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        mod_base       \
        mol_type       \
    
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        Name           \
    
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        non_cytoplasm_location \
    
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        non_cytoplasmic_polypeptide_region \
    
        Note           \
    
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        note           \
    
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        Ontology_term  \
    
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        operon         \
        organell       \
    
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        orthologous_to \
        paralogous_to  \
    
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        Parent         \
    
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        PCR_conditions \
        plasmid        \
    
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        PlasmoAP_score \
    
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        pop_variant    \
    
        previous_systematic_id \
    
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        primary_name \
    
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        product        \
    
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        product_synonym \
    
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        protein_id     \
        replace        \
        results        \
        segment        \
        sequenced_mol  \
        serotype       \
        serovar        \
        sex            \
    
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        signal_anchor_probability \
    
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        signal_peptide \
    
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        signal_peptide_probability \
        SignalP_prediction \
    
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        similarity     \
    
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        source         \
    
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        specific_host  \
    
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        specimen_voucher \
        standard_name  \
        strain         \
        sub_clone      \
        sub_species    \
        sub_strain     \
    
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        synonym \
        systematic_id \
    
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        Target         \
    
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        temporary_systematic_id \
    
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        timelastmodified  \
        tissue_lib     \
        tissue_type    \
    
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        transmembrane  \
    
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        transmembrane_polypeptide_region  \
    
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        transgenic     \
        translation
    
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    # 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.
    
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    #
    # /nfs/pathsoft/databases/GO/new
    # /nfs/pathsoft/databases/protein/go_all
    
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    feature_protein_programs = \
    
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        fasta %uniprot \
        fasta %uniprot_archaea \
        fasta %uniprot_bacteria \
        fasta %uniprot_eukaryota \
        fasta %uniprot_viruses \
        fasta %uniprot_rest \
        fasta %malaria \
        fasta %kineto_aa \
    
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        sigcleave 0 \
        pepstats - \
    
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        blastp uniprot \
        blastp uniprot_archaea \
        blastp uniprot_bacteria \
        blastp uniprot_eukaryota \
        blastp uniprot_viruses \
        blastp uniprot_rest \
        blastp /lustre/scratch101/blastdb/Pathogen/Kineto_aa \
    
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        tblastn %embl_other \
    
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        hth - \
        smart - \
        clustalx PROTEIN \
    
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        jalview PROTEIN
    
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    feature_dna_programs = \
    
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        tblastx %embl_other \
        blastn %embl_other \
    
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        blastx %uniprot \
    
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        fastx %uniprot \
    
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        clustalx DNA
    
    application_programs = \
    
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        jalview
    
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    ncbi_dna_search = \
    
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       blastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=on&BLAST_PROGRAMS=blastn&PAGE_TYPE=BlastSearch&DATABASE=nr&SHOW_DEFAULTS=on&QUERY= \
       blastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY= \
       tblastx http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastx&BLAST_PROGRAMS=tblastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY=
    
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    ncbi_protein_search = \
    
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       blastp http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&QUERY= \
       tblastn http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&QUERY=
    
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    mess_fasta_hits = 10
    
    
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    # 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
    
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    #srs_url = http://srs.ebi.ac.uk/srsbin/cgi-bin/
    srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/
    
    
    # hyperlinked databases in feature editor
    hyperlinks = \
    
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      SWALL+UniProt+UniProtKB srs_url \
      EMBL http://www.ebi.ac.uk/Tools/dbfetch/expasyfetch? \
    
      PubMed+PMID http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch= \
    
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      InterPro http://www.ebi.ac.uk/interpro/entry/ \
    
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      OrthoMCLDB http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=groupList&type=ackeyword&in=Accession&q= \
    
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      PlasmoDB http://plasmodb.org/plasmodb/servlet/sv?page=gene&source_id= \
    
      Pfam http://pfam.sanger.ac.uk/family?acc= \
      SMART http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN= \
    
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      Prosite http://www.expasy.org/prosite/ \
      ProDom http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query= \
      PIRSF http://pir.georgetown.edu/cgi-bin/ipcSF?id= \
      TIGR_TIGRFAMS http://cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc= \
    
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      OPI http://chemlims.com/OPI/MServlet.ChemInfo?module=GeneGo&act=findGenes&Gene_Name_= \
    
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      GO http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO: \
    
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      PANTHER http://www.pantherdb.org/panther/family.do?clsAccession= \
    
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      Superfamily http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid= \
    
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      PDB http://www.rcsb.org/pdb/explore.do?structureId= \
    
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      AID http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid= \
    
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      GeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids= \
    
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      Rfam http://rfam.sanger.ac.uk/family/ \
      GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val=
    
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    # BamView
    # No. threads used to read from multiple BAM files
    bam_read_thread = 2
    # Max read coverage to display
    
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    bam_max_coverage = 1000000
    
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    #
    # CHADO DATABASE OPTIONS 
    #
    
    # chado gene model features default types
    chado_exon_model=CDS
    
    
    # infer CDS and UTR features from gene model
    
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    chado_infer_CDS_UTR=no
    
    #chado_transcript=transcript
    
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    # provide a list of available servers
    #chado_servers = \
    #  malaria_workshop localhost:10101/malaria_workshop?pathdb \
    #  bigtest localhost:10120/test?pathdb
    
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    # define how product qualifiers are stored (as a cv or as a featureprop)
    
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    product_cv=yes
    
    product_cvname = genedb_products
    # cv containing synonym names
    synonym_cvname = genedb_synonym_type
    
    # cv containing annotation types for history qualifier
    history_cvname = annotation_change
    
    # automatically add a history qualifier when a new CV term (product, 
    # GO, controlled curation) term is added to the annotation
    automatic_history_annotation=yes
    
    
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    # set default delete behaviour to make things obsolete, if
    # this is not provided the default is to permanently delete
    set_obsolete_on_delete=yes
    
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    # list of features to record residues for in the database
    # - these are included when inserting or updating their featurelocs
    
    sequence_update_features = polypeptide mRNA rRNA tRNA snRNA snoRNA