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Commit f198a9e0 authored by tjc's avatar tjc
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update polypeptide qualifiers 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8425 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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etc/feature_keys_gff
+ 1
− 1
View file @ f198a9e0
......@@ -11,7 +11,7 @@ region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ont
#chromosome ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified note comment description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score
gene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
#CDS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified codon_start description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score results note comment job
polypeptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref product molecule_type size organism_name strain topology localization gff_source gff_seqname score mass isoelectric charge source private
polypeptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref product molecule_type size organism_name strain topology localization gff_source gff_seqname score mass isoelectric charge source private signal_peptide membrane_structure cytoplasm_location transmembrane non_cytoplasm_location GPI_anchor_cleavage_site
pseudogene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private
pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score product
......
etc/options
+ 12
− 2
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......@@ -2,7 +2,7 @@
# (Note that comment lines start with a hash (#) symbol)
# $Header: //tmp/pathsoft/artemis/etc/options,v 1.48 2008-07-24 15:58:31 tjc Exp $
# $Header: //tmp/pathsoft/artemis/etc/options,v 1.49 2008-08-01 12:41:46 tjc Exp $
# This file should contain option settings that look like this:
#
......@@ -654,6 +654,7 @@ invisible_qualifiers_gff= \
controlled_curation \
country \
cultivar \
cytoplasm_location \
DNA_transposon \
Derives_from \
dev_stage \
......@@ -670,6 +671,7 @@ invisible_qualifiers_gff= \
gff_seqname \
gff_source \
GO \
GPI_anchor_cleavage_site \
ID \
insertion_seq \
isoelectric \
......@@ -681,9 +683,11 @@ invisible_qualifiers_gff= \
macronuclear \
map \
mass \
membrane_structure \
mod_base \
mol_type \
Name \
non_cytoplasm_location \
Note \
note \
Ontology_term \
......@@ -705,6 +709,7 @@ invisible_qualifiers_gff= \
serotype \
serovar \
sex \
signal_peptide \
similarity \
source \
specific_host \
......@@ -721,6 +726,7 @@ invisible_qualifiers_gff= \
timelastmodified \
tissue_lib \
tissue_type \
transmembrane \
transgenic \
translation
......@@ -790,7 +796,11 @@ hyperlinks = \
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= \
Prosite http://www.expasy.org/prosite/
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_=
# chado gene model features default types
chado_exon_model=CDS
......
etc/qualifier_types_gff
+ 6
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......@@ -63,6 +63,7 @@ comment no "text"
cons_splice yes (::) 5'site 3'site
country no "text"
cultivar no "text"
cytoplasm_location no "text"
db_xref no "text"
dev_stage no "text"
direction yes list LEFT RIGHT BOTH
......@@ -77,6 +78,7 @@ frequency yes real 0.0 1.0
function yes "text"
gene no "text"
germline yes none
GPI_anchor_cleavage_site no "text"
haplotype no "text"
insertion_seq no "text"
isolation_source no "text"
......@@ -87,8 +89,10 @@ lab_host no "text"
locus_tag no "text"
macronuclear no none
map no "text"
membrane_structure no "text"
mod_base no modbase
mol_type no "text"
non_cytoplasm_location no "text"
note no "text"
number yes number 1 99999999
operon no "text"
......@@ -117,6 +121,7 @@ sequenced_mol no "list" "cDNA" "cDNA to genomic RNA" \
serotype no "text"
serovar no "text"
sex no "text"
signal_peptide no "text"
specific_host no "text"
specimen_voucher no "text"
standard_name no "text"
......@@ -129,4 +134,5 @@ tissue_lib no "text"
tissue_type no "text"
transgenic no "text"
translation no "text"
transmembrane no "text"
DNA_transposon no "text"
\ No newline at end of file
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