# The standard options file for Artemis

# (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 = 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://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
#

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 \
     Pterobranchia_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 = ttg att atc ata atg gtg
#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

# 24. Pterobranchia mitochondrial
translation_table_24 = \
      agas aggk tgaw

start_codons_24 = ttg ctg 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 gff3 feature feat \
   art artemis

# suffixes used on files that contain sequence - used in file requesters
sequence_file_suffixes = embl gbk genbank gff gff3 tab_embl seq dna dat \
   art artemis fa fasta fas gb fna ffn

# the default height for the base plot window
base_plot_height = 100


# 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


# 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

# features to show on the frame line
#frame_line_features =  \
#  CDS \
#  polypeptide

# 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

# 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

# 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 Name synonym systematic_id \
    temporary_systematic_id gene locus_tag label 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 ID Name


# this list is added to the qualifiers from the qualifier_types file
extra_qualifiers = \
    alias "text" \
    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" \
    pseudo none \
    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 = \
    alias "text" \
    blast_score text \
    blast_file "text" \
    blastn_file "text" \
    blastp_file "text" \
    blastp+go_file "text" \
    blastx_file "text" \
    cluster "text" \
    colour text \
    color text \
    controlled_curation "text" \
    fasta_file "text" \
    GO "text" \
    history "text" \
    literature "text" \
    note "text" \
    orthologous_to "text" \
    paralogous_to "text" \
    polypeptide_domain "text" \
    previous_systematic_id "text" \
    primary_name "text" \
    product_synonym "text" \
    similarity "text" \
    stop_codon_redefined_as_selenocysteine none \
    synonym "text" \
    systematic_id "text" \
    temporary_systematic_id "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  \
    pseudo         \
    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= \
	Alias          \
	allele         \
	bound_moiety   \
	cell_line      \
	cell_type      \
	charge         \
	chromosome     \
    class          \
    clone          \
    clone_lib      \
    cluster        \
    controlled_curation \
    country        \
    cultivar       \
    cytoplasm_location \
    cytoplasmic_polypeptide_region \
    Dbxref \
    DNA_transposon \
    Derives_from   \
    dev_stage      \
    ecotype        \
    environmental_sample \
    estimated_length     \
    exception      \
    feature_id     \
    feature_relationship_rank \
    focus          \
    Gap            \
    gff_feature    \
    gff_group      \
    gff_seqname    \
    gff_source     \
    GO             \
    GPI_anchored \
    GPI_anchor_cleavage_site \
    history \
    ID             \
    insertion_seq  \
    isObsolete \
    isoelectric    \
    isolation_source \
    isolate        \
    kinetoplast    \
    lab_host       \
    literature     \
    locus_tag      \
    macronuclear   \
    map            \
    mass           \
    membrane_structure \
    mod_base       \
    mol_type       \
    Name           \
    non_cytoplasm_location \
    non_cytoplasmic_polypeptide_region \
    Note           \
    note           \
    Ontology_term  \
    operon         \
    organell       \
    orthologous_to \
    paralogous_to  \
    Parent         \
    PCR_conditions \
    plasmid        \
    PlasmoAP_score \
    pop_variant    \
    previous_systematic_id \
    primary_name \
    product        \
    product_synonym \
    protein_id     \
    replace        \
    results        \
    segment        \
    sequenced_mol  \
    serotype       \
    serovar        \
    sex            \
    signal_anchor_probability \
    signal_peptide \
    signal_peptide_probability \
    SignalP_prediction \
    similarity     \
    source         \
    specific_host  \
    specimen_voucher \
    standard_name  \
    strain         \
    sub_clone      \
    sub_species    \
    sub_strain     \
    synonym \
    systematic_id \
    Target         \
    temporary_systematic_id \
    timelastmodified  \
    tissue_lib     \
    tissue_type    \
    transmembrane  \
    transmembrane_polypeptide_region  \
    transgenic     \
    translation


# 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.
#
feature_protein_programs = \
    blastp uniprot \
    blastp uniprot_archaea \
    blastp uniprot_bacteria \
    blastp uniprot_eukaryota \
    blastp uniprot_viruses \
    tblastn %embl_other \
    hth - \
    sigcleave 0 \
    pepstats - \
    clustalx PROTEIN

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

application_programs =

ncbi_dna_search = \
   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=

ncbi_protein_search = \
   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=

interpro_search_url = https://www.ebi.ac.uk/interpro/

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
srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/

# hyperlinked databases in feature editor
hyperlinks = \
  SWALL 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= \
  InterPro http://www.ebi.ac.uk/interpro/entry/ \
  OrthoMCLDB http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=groupList&type=ackeyword&in=Accession&q= \
  PlasmoDB http://plasmodb.org/plasmodb/servlet/sv?page=gene&source_id= \
  Pfam https://pfam.xfam.org/family/ \
  SMART http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN= \
  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= \
  OPI http://chemlims.com/OPI/MServlet.ChemInfo?module=GeneGo&act=findGenes&Gene_Name_= \
  GO http://amigo.geneontology.org/amigo/term/GO: \
  PANTHER http://www.pantherdb.org/panther/family.do?clsAccession= \
  Superfamily http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid= \
  PDB http://www.rcsb.org/pdb/explore.do?structureId= \
  AID http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid= \
  GeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids= \
  Rfam http://rfam.sanger.ac.uk/family/ \
  GI http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val= \
  UniProt https://www.uniprot.org/uniprot/ \
  UniProtKB https://www.uniprot.org/uniprot/ \
  TCDB http://www.tcdb.org/search/result.php?tc=

# BamView
# No. threads used to read from multiple BAM files
bam_read_thread = 2
# Max read coverage to display
bam_max_coverage = 1000000
bamview_ftp_buffer_size=10485760
bamview_use_htsjdk_file_index_caching=true

#
# CHADO DATABASE OPTIONS 
#
# chado gene model features default types
chado_exon_model=CDS

# infer CDS and UTR features from gene model
chado_infer_CDS_UTR=no
#chado_transcript=transcript

# provide a list of available servers
#chado_servers = \
#  malaria_workshop localhost:10101/malaria_workshop?pathdb \
#  bigtest localhost:10120/test?pathdb

# define how product qualifiers are stored (as a cv or as a featureprop)
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

# set default delete behaviour to make things obsolete, if
# this is not provided the default is to permanently delete
set_obsolete_on_delete=yes

# 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

#
# Used to populate the sources combo box for Go Terms.
# See http://amigo.geneontology.org/xrefs
#
GO_evidence_sources = \
   AgBase \
   AGI_LocusCode \
   AGRICOLA_ID \
   AGRICOLA_IND \
   Alzheimers_University_of_Toronto \
   ApiDB_PlasmoDB \
   APSNET \
   APweb \
   AraCyc \
   ARUK-UCL \
   ASAP \
   ASPGD \
   AspGDID \
   AspGD_LOCUS \
   AspGD_REF \
   BFO \
   BHF-UCL \
   BioCyc \
   BIOMD \
   BIOMDID \
   bioPIXIE_MEFIT \
   BIOSIS \
   BRENDA \
   Broad \
   Broad_MGG \
   Broad_NEUROSPORA \
   BTO \
   CACAO \
   CAFA \
   CAS \
   CASGEN \
   CAS_GEN \
   CASREF \
   CAS_SPC \
   CASSPC \
   CAZY \
   CBS \
   CDD \
   CGDID \
   CGD \
   CGD_LOCUS \
   CGD_REF \
   CGEN \
   CGSC \
   ChEBI \
   CL \
   CO_125 \
   COG \
   COG_Cluster \
   COG_Function \
   COG_Pathway \
   CollecTF \
   ComplexPortal \
   CORIELL \
   CORUM \
   cosmoss_PpV1.2 \
   cribi_vitis \
   dbSNP \
   DDANAT \
   DDBJ \
   DFLAT \
   DictyBase \
   DDB \
   dictyBase_gene_name \
   dictyBase_REF \
   DDB_REF \
   DOI \
   EC \
   EchoBASE \
   ECK \
   ECO \
   EcoCyc \
   ECOCYC_REF \
   EcoGene \
   ECOGENE_G \
   EcoliWiki \
   EMAPA \
   EMBL \
   ENA \
   ensembl \
   ENSEMBL_GeneID \
   ENSEMBL_ProteinID \
   ENSEMBL_TranscriptID \
   EnsemblFungi \
   EnsemblMetazoa \
   EnsemblPlants \
   EnsemblPlants/Gramene \
   EnsemblProtists \
   ENZYME \
   EO_GIT \
   EuPathDB \
   Eurofung \
   FB \
   FLYBASE \
   FBbt \
   FMA \
   FYPO \
   GDB \
   GenBank \
   GB \
   Gene3D \
   GeneDB \
   Genesys-pgr \
   GenProtEC \
   GEO \
   GermOnline \
   GO \
   GO_CENTRAL \
   GO_Noctua \
   GO_REF \
   GOC \
   GOC-OWL \
   gomodel \
   GONUTS \
   GOREL \
   GR \
   GR_gene \
   GR_MUT \
   GR_protein \
   GR_QTL \
   GR_REF \
   GRIMS \
   irri \
   grin \
   GRINDesc \
   H-invDB \
   H-invDB_cDNA \
   H-invDB_locus \
   HAMAP \
   HGNC \
   HGNC_gene \
   HPA \
   HPA_antibody \
   HUGO \
   IMG \
   IMGT_HLA \
   IMGT_LIGM \
   IntAct \
   INTERPRO \
   IPR \
   IPI \
   iPTMnet \
   IRGC \
   IRIC \
   ISBN \
   ISRR \
   ISSN \
   IUPHAR \
   IUPHAR_GPCR \
   IUPHAR_RECEPTOR \
   Jaiswal_Lab \
   TIGR \
   JCVI \
   TIGR_EGAD \
   TIGR_CMR \
   JCVI_CMR \
   JCVI_EGAD \
   JCVI_GenProp \
   TIGR_GenProp \
   JCVI_Medtr \
   JCVI_REF \
   TIGR_REF \
   TIGR_TIGRFAMS \
   JCVI_TIGRFAMS \
   JSTOR \
   KEGG \
   KEGG_ENZYME \
   KEGG_LIGAND \
   KEGG_PATHWAY \
   KEGG_REACTION \
   LIFEdb \
   LIS \
   LOCSVMpsi \
   MA \
   MACSC_REF \
   MaizeGDB \
   MaizeGDB_Locus \
   MaizeGDB_QTL \
   MaizeGDB_REF \
   MaizeGDB_stock \
   MEDLINE \
   MENGO \
   MEROPS \
   MEROPS_fam \
   MSH \
   MESH \
   METACYC \
   MGCSC_GENETIC_STOCKS \
   MGD \
   MGI \
   MIPS_funcat \
   MITRE \
   MO \
   ModBase \
   MTBBASE \
   MultiFun \
   NASC \
   NASC_code \
   NC-IUBMB \
   NCBI NCBI_gi \
   NCBI_GP \
   NCBI_locus_tag \
   NCBI_Gene \
   LocusID \
   NCBIGene \
   GeneID \
   NIF_Subcellular \
   NMPDR \
   NTNU_SB \
   OBI \
   OBO_REL \
   OBO_SF2_PECO \
   OBO_SF2_PO \
   OBO_SF_PO \
   MIM OMIM \
   OMSSA \
   PAINT_REF \
   PAMGO \
   PAMGO_GAT \
   PAMGO_MGG \
   PAMGO_VMD \
   PANTHER \
   ParkinsonsUK-UCL \
   PATO \
   PATRIC \
   PDB \
   PECO_GIT \
   Pfam \
   PfamB \
   PharmGKB \
   PhenoScape \
   PHI \
   PINC \
   PIR \
   PIRSF \
   PLANA_REF \
   Planteome_gene \
   PlantSystematics_image_archive \
   PMCID \
   PMID \
   PubMed \
   PO \
   PO_GIT \
   PO_REF \
   POC \
   PomBase \
   Pompep \
   PPI \
   PRO \
   PR \
   PRINTS \
   ProDom \
   Prosite \
   protein_id \
   PROW \
   PseudoCAP \
   MI \
   PSI-MI \
   PSI-MOD \
   MOD \
   PSO_GIT \
   PSORT \
   pTARGET \
   PubChem_BioAssay \
   PubChem_Compound \
   PubChem_Substance \
   RAP-DB \
   REAC \
   REACTOME \
   REBASE \
   REFGENOME \
   RefSeq \
   RESID \
   Rfam \
   RAD \
   RGDID \
   RGD \
   RHEA \
   RiceSES \
   RNAcentral \
   RNAmods \
   RNAMDB \
   RO \
   Roslin_Institute \
   RI \
   SABIO-RK \
   Sanger \
   SEED \
   SGDID \
   SGD \
   SGD_LOCUS \
   SGD_REF \
   SGN \
   SGN_gene \
   SGN_germplasm \
   SGN_ref \
   SMART \
   SMD \
   SO \
   Soy_gene \
   SOY_QTL \
   SOY_ref \
   SPD \
   SP \
   SPTR \
   SUBTILIST \
   SUBTILISTG \
   SUPERFAMILY \
   SWALL \
   Swiss-Prot \
   SynGO \
   SynGO-UCL \
   SYSCILIA_CCNET \
   TAIR \
   taxon \
   NCBITaxon \
   ncbi_taxid \
   TC \
   TGD \
   TGD_LOCUS \
   TGD_REF \
   TO_GIT \
   SPTREMBL \
   TrEMBL \
   TR \
   MuscleTRAIT \
   TRAIT \
   TRANSFAC \
   TreeGenes \
   UBERON \
   UM-BBD \
   UM-BBD_enzymeID \
   UM-BBD_pathwayID \
   UM-BBD_reactionID \
   UM-BBD_ruleID \
   UniGene \
   UniMod \
   UniParc \
   UniPathway \
   UniProtKB \
   SP_KW \
   UniProtKB-KW \
   UniProtKB-SubCell \
   SP_SL \
   UniRule \
   VBRC \
   VEGA \
   VIDA \
   VMD \
   VZ \
   WormBase \
   WB \
   WB_REF \
   WBbt \
   WBls \
   WBPhenotype \
   Wikipedia \
   Xenbase \
   YeastFunc \
   ZFIN



  
