Skip to content
Snippets Groups Projects
Commit bbbfdac6 authored by tjc's avatar tjc
Browse files

gff3 features and qualifiers 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2419 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent a198d122
No related branches found
No related tags found
No related merge requests found
Show whitespace changes
Inline Side-by-side
etc/feature_keys_gff 0 → 100644
+ 41
− 0
View file @ bbbfdac6
#
# Keys (Column 3: "type") constrained to be either:
# (a) a term from the "lite" sequence ontology, SOFA;
# (b) a SOFA accession number (SO:000000).
#
# key Qualifiers (@=mandatory)
# ======= ========================
region ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
contig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
supercontig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
chromosome ID Name Alias Parent Note note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
gene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
CDS ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
polypeptide ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
pseudogene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
intron ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
exon ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score
three_prime_UTR ID Alias Parent Note systematic_id db_xref note
five_prime_UTR ID Alias Parent Note systematic_id db_xref note
transcript
primary_transcript ID Name Alias Parent Note db_xref product note controlled_curation
tRNA ID Name Alias Parent Note db_xref product note controlled_curation
rRNA ID Name Alias Parent Note db_xref product note controlled_curation
mRNA ID Name Alias Parent Note db_xref product note controlled_curation
snRNA ID Name Alias Parent Note db_xref product note controlled_curation
scRNA ID Name Alias Parent Note db_xref product note controlled_curation
snoRNA ID Name Alias Parent Note db_xref product note controlled_curation
polypeptide_domain ID Name Alias Parent Note
signal_peptide ID Name Alias Parent Note
matches ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score
translated_nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
protein_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
sequence_difference ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
repeat_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
direct_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
inverted_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
dispersed_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term
repeat_family ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score
transposable_element ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term
binding_site ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term
etc/qualifier_types_gff 0 → 100644
+ 125
− 0
View file @ bbbfdac6
# Feature qualifiers for EMBL/GenBank feature tables
#
# From: http://www.ebi.ac.uk/~faruque/art/keyqual.txt
#
# valid qualifier types are:
# (::) (text:text,text:text)
# EC "n.n.n.n"
# feature dbname::accno:location
# item single text item
# list one of the listed values
# modbase one of the stored modbase values
# none no value
# number nn
# (other) (text)
# location a valid location range (or feature label)
# real n.n within specified range
# ref [nn]
# text any text, no quotes added, spaces allowed if quoted
# "text" quoted text, double any contained quotes
# "opt" optional quoted text, double any contained quotes
# "list" quoted text, list of accepted values
#
# if not specified, the default is text (so anything is accepted)
#
# Name required Type Value(s) ..
ID no text
Name no text
Alias no text
Parent no text
Note no "text"
description no text
Ontology_term no text
gff_source no text
gff_seqname no text
score no text
Target no text
Gap no text
Derives_from no text
Dbxref no "text"
#
allele no "text"
anticodon yes (::) pos aa
bound_moiety no "text"
cell_line no "text"
cell_type no "text"
chromosome no "opt"
citation no ref
clone no "text"
clone_lib no "text"
codon no (::) seq aa
codon_start yes number 1 3
cons_splice yes (::) 5'site 3'site
country no "text"
cultivar no "text"
db_xref no "text"
dev_stage no "text"
direction yes list LEFT RIGHT BOTH
ecotype no "text"
EC_number no "text"
environmental_sample no none
estimated_length no "text"
evidence yes list EXPERIMENTAL NOT_EXPERIMENTAL
exception no "text"
focus no none
frequency yes real 0.0 1.0
function yes "text"
gene no "text"
germline yes none
haplotype no "text"
insertion_seq no "text"
isolation_source no "text"
isolate no "text"
kinetoplast no "opt"
label yes item
lab_host no "text"
locus_tag no "text"
macronuclear no none
map no "text"
mod_base no modbase
mol_type no "text"
note no "text"
number yes number 1 99999999
operon no "text"
organell no "text"
organism yes "text"
partial yes none
PCR_conditions no "text"
phenotype no "text"
plasmid no "text"
pop_variant no "text"
product no "text"
protein_id no "text"
proviral yes none
pseudo yes none
rearranged yes none
replace no "text"
rpt_family no "text"
rpt_type no list TANDEM INVERTED FLANKING TERMINAL DIRECT \
DISPERSED OTHER
rpt_unit no location
segment no "text"
sequenced_mol no "list" "cDNA" "cDNA to genomic RNA" \
"cDNA to mRNA" "cDNA to other RNA" \
"cDNA to rRNA" "DNA" "mRNA" \
"RNA" "rRNA" "scRNA" "snRNA" "tRNA"
serotype no "text"
serovar no "text"
sex no "text"
specific_host no "text"
specimen_voucher no "text"
standard_name no "text"
strain no "text"
sub_clone no "text"
sub_species no "text"
sub_strain no "text"
tissue_lib no "text"
tissue_type no "text"
transgenic no "text"
translation no "text"
transl_except no (::) pos aa
transl_table no number 1 11
transposon no "text"
usedin no feature
variety no "text"
virion no none
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment