options 23.15 KiB
# The standard options file for Artemis
# (Note that comment lines start with a hash (#) symbol)
# $Header: //tmp/pathsoft/artemis/etc/options,v 1.73 2009-08-06 16:15:19 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://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 = 5colour_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 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.
#
# /nfs/pathsoft/databases/GO/new
# /nfs/pathsoft/databases/protein/go_allfeature_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 /lustre/scratch101/blastdb/Pathogen/Kineto_aa \
tblastn %embl_other \
hth - \
smart - \
clustalx PROTEIN \
jalview PROTEIN
feature_dna_programs = \
tblastx %embl_other \
blastn %embl_other \
blastx %uniprot \
fastx %uniprot \
clustalx DNA
application_programs = \
jalview
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=
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://srs.ebi.ac.uk/srsbin/cgi-bin/
srs_url = http://www.bioinformatics.nl/srsbin/cgi-bin/
# hyperlinked databases in feature editor
hyperlinks = \
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= \
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= \
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