ENUMERATED | { |
contains | 1 |
equals | 2 |
starts | 3 |
ends | 4 |
inlist | 5 |
} |
SEQUENCE | { |
word | VisibleString OPTIONAL |
synonyms | SET OF VisibleString OPTIONAL |
case-sensitive | BOOLEAN DEFAULT false |
whole-word | BOOLEAN DEFAULT false |
} |
SEQUENCE | { |
match-text | VisibleString OPTIONAL |
match-location | String-location DEFAULT contains |
case-sensitive | BOOLEAN DEFAULT false |
ignore-space | BOOLEAN DEFAULT false |
ignore-punct | BOOLEAN DEFAULT false |
ignore-words | Word-substitution-set OPTIONAL |
whole-word | BOOLEAN DEFAULT false |
not-present | BOOLEAN DEFAULT false |
is-all-caps | BOOLEAN DEFAULT false |
is-all-lower | BOOLEAN DEFAULT false |
is-all-punct | BOOLEAN DEFAULT false |
ignore-weasel | BOOLEAN DEFAULT false |
} |
ENUMERATED | { |
any | 0 |
plus | 1 |
minus | 2 |
} |
ENUMERATED | { |
any | 0 |
nuc | 1 |
prot | 2 |
} |
ENUMERATED | { |
either | 0 |
partial | 1 |
complete | 2 |
} |
ENUMERATED | { |
any | 0 |
single-interval | 1 |
joined | 2 |
ordered | 3 |
} |
CHOICE | { |
dist-from-end | INTEGER |
max-dist-from-end | INTEGER |
min-dist-from-end | INTEGER |
} |
SEQUENCE | { |
strand | Strand-constraint DEFAULT any |
seq-type | Seqtype-constraint DEFAULT any |
partial5 | Partial-constraint DEFAULT either |
partial3 | Partial-constraint DEFAULT either |
location-type | Location-type-constraint DEFAULT any |
end5 | Location-pos-constraint OPTIONAL |
end3 | Location-pos-constraint OPTIONAL |
} |
ENUMERATED | { |
any | 0 |
feature | 1 |
descriptor | 2 |
} |
ENUMERATED | { |
any | 0 |
gene | 1 |
org | 2 |
cds | 3 |
prot | 4 |
preRNA | 5 |
mRNA | 6 |
tRNA | 7 |
rRNA | 8 |
snRNA | 9 |
scRNA | 10 |
otherRNA | 11 |
pub | 12 |
seq | 13 |
imp | 14 |
allele | 15 |
attenuator | 16 |
c-region | 17 |
caat-signal | 18 |
imp-CDS | 19 |
conflict | 20 |
d-loop | 21 |
d-segment | 22 |
enhancer | 23 |
exon | 24 |
gC-signal | 25 |
iDNA | 26 |
intron | 27 |
j-segment | 28 |
ltr | 29 |
mat-peptide | 30 |
misc-binding | 31 |
misc-difference | 32 |
misc-feature | 33 |
misc-recomb | 34 |
misc-RNA | 35 |
misc-signal | 36 |
misc-structure | 37 |
modified-base | 38 |
mutation | 39 |
n-region | 40 |
old-sequence | 41 |
polyA-signal | 42 |
polyA-site | 43 |
precursor-RNA | 44 |
prim-transcript | 45 |
primer-bind | 46 |
promoter | 47 |
protein-bind | 48 |
rbs | 49 |
repeat-region | 50 |
rep-origin | 51 |
s-region | 52 |
sig-peptide | 53 |
source | 54 |
stem-loop | 55 |
sts | 56 |
tata-signal | 57 |
terminator | 58 |
transit-peptide | 59 |
unsure | 60 |
v-region | 61 |
v-segment | 62 |
variation | 63 |
virion | 64 |
n3clip | 65 |
n3UTR | 66 |
n5clip | 67 |
n5UTR | 68 |
n10-signal | 69 |
n35-signal | 70 |
site-ref | 71 |
region | 72 |
comment | 73 |
bond | 74 |
site | 75 |
rsite | 76 |
user | 77 |
txinit | 78 |
num | 79 |
psec-str | 80 |
non-std-residue | 81 |
het | 82 |
biosrc | 83 |
preprotein | 84 |
mat-peptide-aa | 85 |
sig-peptide-aa | 86 |
transit-peptide-aa | 87 |
snoRNA | 88 |
gap | 89 |
operon | 90 |
oriT | 91 |
ncRNA | 92 |
tmRNA | 93 |
mobile-element | 94 |
} |
ENUMERATED | { |
allele | 1 |
activity | 2 |
anticodon | 3 |
bound-moiety | 4 |
chromosome | 5 |
citation | 6 |
codon | 7 |
codon-start | 8 |
codons-recognized | 9 |
compare | 10 |
cons-splice | 11 |
db-xref | 12 |
description | 13 |
direction | 14 |
ec-number | 15 |
environmental-sample | 16 |
evidence | 17 |
exception | 18 |
experiment | 19 |
focus | 20 |
frequency | 21 |
function | 22 |
gene | 23 |
gene-description | 24 |
inference | 25 |
label | 26 |
locus-tag | 27 |
map | 28 |
mobile-element | 29 |
mod-base | 30 |
mol-type | 31 |
ncRNA-class | 32 |
note | 33 |
number | 34 |
old-locus-tag | 35 |
operon | 36 |
organism | 37 |
organelle | 38 |
partial | 39 |
phenotype | 40 |
plasmid | 41 |
product | 42 |
protein-id | 43 |
pseudo | 44 |
rearranged | 45 |
replace | 46 |
rpt-family | 47 |
rpt-type | 48 |
rpt-unit | 49 |
rpt-unit-seq | 50 |
rpt-unit-range | 51 |
segment | 52 |
sequenced-mol | 53 |
standard-name | 54 |
synonym | 55 |
transcript-id | 56 |
transgenic | 57 |
translation | 58 |
transl-except | 59 |
transl-table | 60 |
usedin | 61 |
mobile-element-type | 62 |
mobile-element-name | 63 |
gene-comment | 64 |
satellite | 65 |
satellite-type | 66 |
satellite-name | 67 |
location | 68 |
tag-peptide | 69 |
mobile-element-type-type | 70 |
name | 71 |
pcr-conditions | 72 |
} |
SEQUENCE | { |
qual | Feat-qual-legal |
val | VisibleString |
} |
CHOICE | { |
qual | Feat-qual-legal-val |
} |
CHOICE | { |
legal-qual | Feat-qual-legal |
illegal-qual | String-constraint |
} |
SEQUENCE | { |
type | Macro-feature-type |
field | Feat-qual-choice |
} |
SEQUENCE | { |
type | Macro-feature-type |
field | Feat-qual-legal |
} |
SEQUENCE | { |
type | Macro-feature-type |
field-from | Feat-qual-choice |
field-to | Feat-qual-choice |
} |
CHOICE | { |
any | NULL |
preRNA | NULL |
mRNA | NULL |
tRNA | NULL |
rRNA | NULL |
ncRNA | VisibleString |
tmRNA | NULL |
miscRNA | NULL |
} |
ENUMERATED | { |
product | 1 |
comment | 2 |
codons-recognized | 3 |
ncrna-class | 4 |
anticodon | 5 |
transcript-id | 6 |
gene-locus | 7 |
gene-description | 8 |
gene-maploc | 9 |
gene-locus-tag | 10 |
gene-synonym | 11 |
gene-comment | 12 |
tag-peptide | 13 |
} |
SEQUENCE | { |
type | Rna-feat-type |
field | Rna-field |
} |
SEQUENCE | { |
type | Rna-feat-type |
field-from | Rna-field |
field-to | Rna-field |
} |
ENUMERATED | { |
acronym | 1 |
anamorph | 2 |
authority | 3 |
bio-material | 4 |
biotype | 5 |
biovar | 6 |
breed | 7 |
cell-line | 8 |
cell-type | 9 |
chemovar | 10 |
chromosome | 11 |
clone | 12 |
clone-lib | 13 |
collected-by | 14 |
collection-date | 15 |
common | 16 |
common-name | 17 |
country | 18 |
cultivar | 19 |
culture-collection | 20 |
dev-stage | 21 |
division | 22 |
dosage | 23 |
ecotype | 24 |
endogenous-virus-name | 25 |
environmental-sample | 26 |
forma | 27 |
forma-specialis | 28 |
frequency | 29 |
fwd-primer-name | 30 |
fwd-primer-seq | 31 |
gb-acronym | 32 |
gb-anamorph | 33 |
gb-synonym | 34 |
genotype | 35 |
germline | 36 |
group | 37 |
haplotype | 38 |
identified-by | 39 |
insertion-seq-name | 40 |
isolate | 41 |
isolation-source | 42 |
lab-host | 43 |
lat-lon | 44 |
lineage | 45 |
map | 46 |
metagenome-source | 47 |
metagenomic | 48 |
old-lineage | 49 |
old-name | 50 |
orgmod-note | 51 |
nat-host | 52 |
pathovar | 53 |
plasmid-name | 54 |
plastid-name | 55 |
pop-variant | 56 |
rearranged | 57 |
rev-primer-name | 58 |
rev-primer-seq | 59 |
segment | 60 |
serogroup | 61 |
serotype | 62 |
serovar | 63 |
sex | 64 |
specimen-voucher | 65 |
strain | 66 |
subclone | 67 |
subgroup | 68 |
subsource-note | 69 |
sub-species | 70 |
substrain | 71 |
subtype | 72 |
synonym | 73 |
taxname | 74 |
teleomorph | 75 |
tissue-lib | 76 |
tissue-type | 77 |
transgenic | 78 |
transposon-name | 79 |
type | 80 |
variety | 81 |
specimen-voucher-INST | 82 |
specimen-voucher-COLL | 83 |
specimen-voucher-SpecID | 84 |
culture-collection-INST | 85 |
culture-collection-COLL | 86 |
culture-collection-SpecID | 87 |
bio-material-INST | 88 |
bio-material-COLL | 89 |
bio-material-SpecID | 90 |
all-notes | 91 |
mating-type | 92 |
linkage-group | 93 |
haplogroup | 94 |
all-quals | 95 |
dbxref | 96 |
taxid | 97 |
all-primers | 98 |
altitude | 99 |
} |
SEQUENCE | { |
field-from | Source-qual |
field-to | Source-qual |
} |
ENUMERATED | { |
unknown | 0 |
genomic | 1 |
chloroplast | 2 |
chromoplast | 3 |
kinetoplast | 4 |
mitochondrion | 5 |
plastid | 6 |
macronuclear | 7 |
extrachrom | 8 |
plasmid | 9 |
transposon | 10 |
insertion-seq | 11 |
cyanelle | 12 |
proviral | 13 |
virion | 14 |
nucleomorph | 15 |
apicoplast | 16 |
leucoplast | 17 |
proplastid | 18 |
endogenous-virus | 19 |
hydrogenosome | 20 |
chromosome | 21 |
chromatophore | 22 |
} |
ENUMERATED | { |
unknown | 0 |
natural | 1 |
natmut | 2 |
mut | 3 |
artificial | 4 |
synthetic | 5 |
other | 255 |
} |
CHOICE | { |
textqual | Source-qual |
location | Source-location |
origin | Source-origin |
gcode | INTEGER |
mgcode | INTEGER |
} |
SEQUENCE | { |
srcqual | Source-qual |
val | VisibleString |
} |
CHOICE | { |
textqual | Source-qual-text-val |
location | Source-location |
origin | Source-origin |
gcode | INTEGER |
mgcode | INTEGER |
} |
ENUMERATED | { |
cds-comment | 1 |
gene-locus | 2 |
gene-description | 3 |
gene-comment | 4 |
gene-allele | 5 |
gene-maploc | 6 |
gene-locus-tag | 7 |
gene-synonym | 8 |
gene-old-locus-tag | 9 |
mrna-product | 10 |
mrna-comment | 11 |
prot-name | 12 |
prot-description | 13 |
prot-ec-number | 14 |
prot-activity | 15 |
prot-comment | 16 |
mat-peptide-name | 17 |
mat-peptide-description | 18 |
mat-peptide-ec-number | 19 |
mat-peptide-activity | 20 |
mat-peptide-comment | 21 |
cds-inference | 22 |
gene-inference | 23 |
codon-start | 24 |
} |
SEQUENCE | { |
field-from | CDSGeneProt-field |
field-to | CDSGeneProt-field |
} |
ENUMERATED | { |
unknown | 0 |
genomic | 1 |
precursor-RNA | 2 |
mRNA | 3 |
rRNA | 4 |
tRNA | 5 |
genomic-mRNA | 6 |
cRNA | 7 |
transcribed-RNA | 8 |
ncRNA | 9 |
transfer-messenger-RNA | 10 |
macro-other | 11 |
} |
ENUMERATED | { |
unknown | 0 |
standard | 1 |
est | 2 |
sts | 3 |
survey | 4 |
genetic-map | 5 |
physical-map | 6 |
derived | 7 |
concept-trans | 8 |
seq-pept | 9 |
both | 10 |
seq-pept-overlap | 11 |
seq-pept-homol | 12 |
concept-trans-a | 13 |
htgs-1 | 14 |
htgs-2 | 15 |
htgs-3 | 16 |
fli-cDNA | 17 |
htgs-0 | 18 |
htc | 19 |
wgs | 20 |
barcode | 21 |
composite-wgs-htgs | 22 |
tsa | 23 |
other | 24 |
} |
ENUMERATED | { |
unknown | 0 |
complete | 1 |
partial | 2 |
no-left | 3 |
no-right | 4 |
no-ends | 5 |
has-left | 6 |
has-right | 7 |
other | 6 |
} |
ENUMERATED | { |
unknown | 0 |
dna | 1 |
rna | 2 |
protein | 3 |
nucleotide | 4 |
other | 5 |
} |
ENUMERATED | { |
unknown | 0 |
linear | 1 |
circular | 2 |
tandem | 3 |
other | 4 |
} |
ENUMERATED | { |
unknown | 0 |
single | 1 |
double | 2 |
mixed | 3 |
mixed-rev | 4 |
other | 5 |
} |
CHOICE | { |
molecule | Molecule-type |
technique | Technique-type |
completedness | Completedness-type |
mol-class | Molecule-class-type |
topology | Topology-type |
strand | Strand-type |
} |
SEQUENCE | { |
from | Molecule-type |
to | Molecule-type |
} |
SEQUENCE | { |
from | Technique-type |
to | Technique-type |
} |
SEQUENCE | { |
from | Completedness-type |
to | Completedness-type |
} |
SEQUENCE | { |
from | Molecule-class-type |
to | Molecule-class-type |
} |
SEQUENCE | { |
from | Topology-type |
to | Topology-type |
} |
SEQUENCE | { |
from | Strand-type |
to | Strand-type |
} |
CHOICE | { |
molecule | Molinfo-molecule-pair |
technique | Molinfo-technique-pair |
completedness | Molinfo-completedness-pair |
mol-class | Molinfo-mol-class-pair |
topology | Molinfo-topology-pair |
strand | Molinfo-strand-pair |
} |
SEQUENCE | { |
field | Molinfo-field |
is-not | BOOLEAN DEFAULT false |
} |
ENUMERATED | { |
cit | 1 |
authors | 2 |
journal | 3 |
volume | 4 |
issue | 5 |
pages | 6 |
date | 7 |
serial-number | 8 |
title | 9 |
affiliation | 10 |
affil-div | 11 |
affil-city | 12 |
affil-sub | 13 |
affil-country | 14 |
affil-street | 15 |
affil-email | 16 |
affil-fax | 17 |
affil-phone | 18 |
affil-zipcode | 19 |
authors-initials | 20 |
pmid | 21 |
pub-class | 22 |
} |
CHOICE | { |
database | NULL |
named | VisibleString |
field-name | NULL |
} |
SEQUENCE | { |
from | Structured-comment-field |
to | Structured-comment-field |
} |
ENUMERATED | { |
genome-project-id | 1 |
comment-descriptor | 2 |
defline | 3 |
keyword | 4 |
} |
ENUMERATED | { |
trace-assembly | 1 |
bio-sample | 2 |
probe-db | 3 |
sequence-read-archve | 4 |
bio-project | 5 |
assembly | 6 |
} |
SEQUENCE | { |
from | DBLink-field-type |
to | DBLink-field-type |
} |
ENUMERATED | { |
any | 0 |
published | 1 |
unpublished | 2 |
in-press | 3 |
submitter-block | 4 |
} |
SEQUENCE | { |
field | Publication-field |
constraint | String-constraint |
} |
CHOICE | { |
is-present | NULL |
is-not-present | NULL |
is-all-caps | NULL |
is-all-lower | NULL |
is-all-punct | NULL |
} |
SEQUENCE | { |
field | Publication-field |
constraint | Pub-field-special-constraint-type |
} |
SEQUENCE | { |
type | Pub-type |
field | Pub-field-constraint OPTIONAL |
special-field | Pub-field-special-constraint OPTIONAL |
} |
SEQUENCE | { |
field1 | Source-qual-choice OPTIONAL |
field2 | Source-qual-choice OPTIONAL |
constraint | String-constraint OPTIONAL |
type-constraint | Object-type-constraint OPTIONAL |
} |
ENUMERATED | { |
gene | 1 |
mRNA | 2 |
cds | 3 |
prot | 4 |
exon | 5 |
mat-peptide | 6 |
} |
SEQUENCE | { |
feature | CDSGeneProt-feature-type-constraint |
is-pseudo | BOOLEAN DEFAULT true |
} |
CHOICE | { |
field | CDSGeneProt-field |
} |
SEQUENCE | { |
field1 | CDSGeneProt-constraint-field OPTIONAL |
field2 | CDSGeneProt-constraint-field OPTIONAL |
constraint | String-constraint OPTIONAL |
} |
SEQUENCE | { |
field | Field-type |
string-constraint | String-constraint |
} |
ENUMERATED | { |
any | 0 |
genomic | 1 |
precursor-RNA | 2 |
mRNA | 3 |
rRNA | 4 |
tRNA | 5 |
genomic-mRNA | 6 |
cRNA | 7 |
transcribed-RNA | 8 |
ncRNA | 9 |
transfer-messenger-RNA | 10 |
} |
CHOICE | { |
any | NULL |
nucleotide | NULL |
dna | NULL |
rna | Sequence-constraint-rnamol |
protein | NULL |
} |
CHOICE | { |
equals | INTEGER |
greater-than | INTEGER |
less-than | INTEGER |
} |
ENUMERATED | { |
any | 0 |
minus-only | 1 |
plus-only | 2 |
at-least-one-minus | 3 |
at-least-one-plus | 4 |
no-minus | 5 |
no-plus | 6 |
} |
SEQUENCE | { |
seqtype | Sequence-constraint-mol-type-constraint OPTIONAL |
id | String-constraint OPTIONAL |
feature | Macro-feature-type |
num-type-features | Quantity-constraint OPTIONAL |
num-features | Quantity-constraint OPTIONAL |
length | Quantity-constraint OPTIONAL |
strandedness | Feature-strandedness-constraint DEFAULT any |
} |
ENUMERATED | { |
dont-care | 0 |
yes | 1 |
no | 2 |
} |
SEQUENCE | { |
actual-strings | String-constraint-set |
transl-strings | String-constraint-set |
internal-stops | Match-type-constraint DEFAULT dont-care |
num-mismatches | Quantity-constraint OPTIONAL |
} |
CHOICE | { |
string | String-constraint |
location | Location-constraint |
field | Field-constraint |
source | Source-constraint |
cdsgeneprot-qual | CDSGeneProt-qual-constraint |
cdsgeneprot-pseudo | CDSGeneProt-pseudo-constraint |
sequence | Sequence-constraint |
pub | Publication-constraint |
molinfo | Molinfo-field-constraint |
field-missing | Field-type |
translation | Translation-constraint |
} |
CHOICE | { |
free-text | VisibleString |
digits | NULL |
letters | NULL |
} |
SEQUENCE | { |
left-marker | Text-marker OPTIONAL |
include-left | BOOLEAN |
right-marker | Text-marker OPTIONAL |
include-right | BOOLEAN |
inside | BOOLEAN |
case-sensitive | BOOLEAN DEFAULT false |
whole-word | BOOLEAN DEFAULT false |
} |
ENUMERATED | { |
anywhere | 0 |
beginning | 1 |
end | 2 |
} |
SEQUENCE | { |
find-txt | VisibleString |
repl-txt | VisibleString OPTIONAL |
location | Field-edit-location DEFAULT anywhere |
case-insensitive | BOOLEAN DEFAULT false |
} |
CHOICE | { |
source-qual | Source-qual-choice |
feature-field | Feature-field |
rna-field | Rna-qual |
cds-gene-prot | CDSGeneProt-field |
molinfo-field | Molinfo-field |
pub | Publication-field |
struc-comment-field | Structured-comment-field |
misc | Misc-field |
dblink | DBLink-field-type |
} |
CHOICE | { |
source-qual | Source-qual-pair |
feature-field | Feature-field-pair |
rna-field | Rna-qual-pair |
cds-gene-prot | CDSGeneProt-field-pair |
molinfo-field | Molinfo-field-pair |
struc-comment-field | Structured-comment-field-pair |
dblink | DBLink-field-pair |
} |
ENUMERATED | { |
replace-old | 1 |
append-semi | 2 |
append-space | 3 |
append-colon | 4 |
append-comma | 5 |
append-none | 6 |
prefix-semi | 7 |
prefix-space | 8 |
prefix-colon | 9 |
prefix-comma | 10 |
prefix-none | 11 |
leave-old | 12 |
add-qual | 13 |
} |
SEQUENCE | { |
field | Field-type |
value | VisibleString |
existing-text | ExistingTextOption |
} |
SEQUENCE | { |
edit | Field-edit |
field | Field-type |
} |
ENUMERATED | { |
none | 0 |
tolower | 1 |
toupper | 2 |
firstcap | 3 |
firstcaprestnochange | 4 |
firstlower-restnochange | 5 |
cap-word-space | 6 |
cap-word-space-punc | 7 |
} |
CHOICE | { |
edit | Field-edit |
caps | Cap-change |
remove | Text-portion |
} |
SEQUENCE | { |
fields | Field-pair-type |
strip-name | BOOLEAN DEFAULT false |
keep-original | BOOLEAN DEFAULT false |
capitalization | Cap-change DEFAULT none |
existing-text | ExistingTextOption |
} |
SEQUENCE | { |
fields | Field-pair-type |
existing-text | ExistingTextOption |
} |
SEQUENCE | { |
fields | Field-pair-type |
} |
SEQUENCE | { |
portion | Text-portion |
fields | Field-pair-type |
remove-from-parsed | BOOLEAN DEFAULT false |
remove-left | BOOLEAN DEFAULT false |
remove-right | BOOLEAN DEFAULT false |
transform | Text-transform-set OPTIONAL |
existing-text | ExistingTextOption |
} |
SEQUENCE | { |
field | Field-type |
} |
SEQUENCE | { |
portion | Text-portion |
field | Field-type |
remove-if-not-found | BOOLEAN DEFAULT false |
} |
CHOICE | { |
apply | Apply-action |
edit | Edit-action |
convert | Convert-action |
copy | Copy-action |
swap | Swap-action |
remove | Remove-action |
parse | AECRParse-action |
remove-outside | Remove-outside-action |
} |
SEQUENCE | { |
action | Action-choice |
also-change-mrna | BOOLEAN DEFAULT false |
constraint | Constraint-choice-set OPTIONAL |
} |
CHOICE | { |
source-qual | Source-qual |
taxname-after-binomial | NULL |
} |
SEQUENCE | { |
field | Parse-src-org-choice |
type | Object-type-constraint DEFAULT any |
} |
CHOICE | { |
whole-text | NULL |
db | NULL |
tag | VisibleString |
} |
CHOICE | { |
defline | NULL |
flatfile | NULL |
local-id | NULL |
org | Parse-src-org |
comment | NULL |
bankit-comment | NULL |
structured-comment | VisibleString |
file-id | NULL |
general-id | Parse-src-general-id |
} |
SEQUENCE | { |
field | Source-qual-choice |
type | Object-type-constraint DEFAULT any |
} |
CHOICE | { |
defline | NULL |
org | Parse-dst-org |
featqual | Feature-field-legal |
comment-descriptor | NULL |
dbxref | VisibleString |
} |
SEQUENCE | { |
portion | Text-portion |
src | Parse-src |
dest | Parse-dest |
capitalization | Cap-change DEFAULT none |
remove-from-parsed | BOOLEAN DEFAULT false |
transform | Text-transform-set OPTIONAL |
existing-text | ExistingTextOption |
} |
SEQUENCE | { |
from | INTEGER |
to | INTEGER |
} |
CHOICE | { |
interval | Location-interval |
whole-sequence | NULL |
point | INTEGER |
} |
CHOICE | { |
list | Sequence-list |
all | NULL |
} |
SEQUENCE | { |
type | Macro-feature-type |
partial5 | BOOLEAN DEFAULT false |
partial3 | BOOLEAN DEFAULT false |
plus-strand | BOOLEAN DEFAULT true |
location | Location-choice |
seq-list | Sequence-list-choice |
add-redundant | BOOLEAN DEFAULT true |
add-mrna | BOOLEAN DEFAULT false |
apply-to-parts | BOOLEAN DEFAULT false |
only-seg-num | INTEGER DEFAULT -1 |
fields | Feat-qual-legal-set OPTIONAL |
src-fields | Source-qual-val-set OPTIONAL |
} |
SEQUENCE | { |
type | Macro-feature-type |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
remove-mRNA | BOOLEAN |
remove-gene | BOOLEAN |
remove-transcript-id | BOOLEAN |
} |
CHOICE | { |
cds | Convert-from-CDS-options |
} |
ENUMERATED | { |
disulfide | 1 |
thioester | 2 |
crosslink | 3 |
thioether | 4 |
other | 5 |
} |
ENUMERATED | { |
active | 1 |
binding | 2 |
cleavage | 3 |
inhibit | 4 |
modified | 5 |
glycosylation | 6 |
myristoylation | 7 |
mutagenized | 8 |
metal-binding | 9 |
phosphorylation | 10 |
acetylation | 11 |
amidation | 12 |
methylation | 13 |
hydroxylation | 14 |
sulfatation | 15 |
oxidative-deamination | 16 |
pyrrolidone-carboxylic-acid | 17 |
gamma-carboxyglutamic-acid | 18 |
blocked | 19 |
lipid-binding | 20 |
np-binding | 21 |
dna-binding | 22 |
signal-peptide | 23 |
transit-peptide | 24 |
transmembrane-region | 25 |
nitrosylation | 26 |
other | 27 |
} |
SEQUENCE | { |
create-nucleotide | BOOLEAN |
} |
CHOICE | { |
bond | Bond-type |
site | Site-type |
region | Region-type |
ncrna-class | VisibleString |
remove-original | BOOLEAN |
} |
SEQUENCE | { |
type-from | Macro-feature-type |
type-to | Macro-feature-type |
src-options | Convert-feature-src-options OPTIONAL |
dst-options | Convert-feature-dst-options OPTIONAL |
leave-original | BOOLEAN |
src-feat-constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
any | 0 |
plus | 1 |
minus | 2 |
unknown | 3 |
both | 4 |
} |
ENUMERATED | { |
plus | 1 |
minus | 2 |
unknown | 3 |
both | 4 |
reverse | 5 |
} |
SEQUENCE | { |
strand-from | Feature-location-strand-from |
strand-to | Feature-location-strand-to |
} |
ENUMERATED | { |
all | 0 |
at-end | 1 |
bad-start | 2 |
frame-not-one | 3 |
} |
SEQUENCE | { |
constraint | Partial-5-set-constraint |
extend | BOOLEAN |
} |
ENUMERATED | { |
all | 0 |
not-at-end | 1 |
good-start | 2 |
} |
ENUMERATED | { |
all | 0 |
at-end | 1 |
bad-end | 2 |
} |
SEQUENCE | { |
constraint | Partial-3-set-constraint |
extend | BOOLEAN |
} |
ENUMERATED | { |
all | 0 |
not-at-end | 1 |
good-end | 2 |
} |
ENUMERATED | { |
all | 0 |
at-end | 1 |
} |
SEQUENCE | { |
constraint | Partial-both-set-constraint |
extend | BOOLEAN |
} |
ENUMERATED | { |
all | 0 |
not-at-end | 1 |
} |
ENUMERATED | { |
join | 1 |
order | 2 |
merge | 3 |
} |
SEQUENCE | { |
type | Macro-feature-type |
include-feat | BOOLEAN |
distance | Quantity-constraint OPTIONAL |
} |
CHOICE | { |
strand | Edit-location-strand |
set-5-partial | Partial-5-set-action |
clear-5-partial | Partial-5-clear-constraint |
set-3-partial | Partial-3-set-action |
clear-3-partial | Partial-3-clear-constraint |
set-both-partial | Partial-both-set-action |
clear-both-partial | Partial-both-clear-constraint |
convert | Convert-location-type |
extend-5 | NULL |
extend-3 | NULL |
extend-5-to-feat | Extend-to-feature |
extend-3-to-feat | Extend-to-feature |
} |
SEQUENCE | { |
type | Macro-feature-type |
action | Location-edit-type |
retranslate-cds | BOOLEAN OPTIONAL |
also-edit-gene | BOOLEAN OPTIONAL |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
to-list | Molinfo-field-list |
from-list | Molinfo-field-list OPTIONAL |
constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
all | 0 |
title | 1 |
source | 2 |
publication | 3 |
comment | 4 |
genbank | 5 |
user | 6 |
create-date | 7 |
update-date | 8 |
mol-info | 9 |
structured-comment | 10 |
genome-project-id | 11 |
} |
SEQUENCE | { |
type | Descriptor-type |
constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
feature-list | 1 |
complete-sequence | 2 |
complete-genome | 3 |
sequence | 4 |
} |
ENUMERATED | { |
use-comment-before-first-semicolon | 1 |
look-for-noncoding-products | 2 |
} |
SEQUENCE | { |
modifiers | SET OF Source-qual OPTIONAL |
clause-list-type | Autodef-list-type |
misc-feat-parse-rule | Autodef-misc-feat-parse-rule DEFAULT look-for-noncoding-products |
} |
SEQUENCE | { |
title | BOOLEAN OPTIONAL |
authors | BOOLEAN OPTIONAL |
affiliation | BOOLEAN OPTIONAL |
affil-country | BOOLEAN OPTIONAL |
punct-only | BOOLEAN DEFAULT false |
constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
short-to-long | 1 |
long-to-short | 2 |
alphabetical | 3 |
} |
SEQUENCE | { |
field | Field-type |
order | Sort-order |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
last-name-only | BOOLEAN |
} |
CHOICE | { |
pub | Fix-pub-caps-action |
src-country | NULL |
mouse-strain | NULL |
src-qual | Source-qual |
author | Fix-author-caps |
} |
CHOICE | { |
collection-date | NULL |
lat-lon | NULL |
primers | NULL |
protein-name | NULL |
} |
SEQUENCE | { |
type | Macro-feature-type |
ignore-partials | BOOLEAN |
case-sensitive | BOOLEAN |
remove-proteins | BOOLEAN |
rd-constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
any | 0 |
suppressing | 1 |
non-suppressing | 2 |
} |
ENUMERATED | { |
any | 0 |
necessary | 1 |
unnecessary | 2 |
} |
SEQUENCE | { |
feature | Macro-feature-type |
suppression | Gene-xref-suppression-type |
necessary | Gene-xref-necessary-type |
} |
CHOICE | { |
gene | Gene-xref-type |
} |
SEQUENCE | { |
xref-type | Xref-type |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
feature | Macro-feature-type |
constraint | Constraint-choice-set OPTIONAL |
} |
ENUMERATED | { |
truncate-middle-initials | 1 |
strip-suffix | 2 |
move-middle-to-first | 3 |
} |
SEQUENCE | { |
fix-type | Author-fix-type |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
filename | VisibleString |
add-cit-subs | BOOLEAN DEFAULT false |
} |
CHOICE | { |
local-id | NULL |
defline | Text-portion |
} |
SEQUENCE | { |
src | Create-TSA-ids-src |
suffix | VisibleString OPTIONAL |
id-text-portion | Text-portion OPTIONAL |
} |
SEQUENCE | { |
test-name | VisibleString |
} |
CHOICE | { |
remove-single-item-set | NULL |
renormalize-nuc-prot-sets | NULL |
fix-pop-to-phy | NULL |
} |
CHOICE | { |
feature-id | NULL |
gene-locus-tag | NULL |
protein-id | NULL |
dbxref | NULL |
nuc-id | NULL |
src-qual | Source-qual-choice |
protein-name | NULL |
any | NULL |
} |
SEQUENCE | { |
match-type | Table-match-type |
match-location | String-location DEFAULT equals |
} |
CHOICE | { |
table | NULL |
} |
SEQUENCE | { |
filename | VisibleString |
match-type | Table-match |
in-memory-table | Apply-table-extra-data OPTIONAL |
also-change-mrna | BOOLEAN DEFAULT false |
skip-blanks | BOOLEAN DEFAULT true |
} |
SEQUENCE | { |
filename | VisibleString |
in-memory-table | Apply-table-extra-data OPTIONAL |
} |
SEQUENCE | { |
descriptor-list | Add-file-action |
constraint | Constraint-choice-set OPTIONAL |
} |
SEQUENCE | { |
constraint | Constraint-choice-set |
} |
SEQUENCE | { |
delete-improper-format | BOOLEAN |
delete-unrecognized | BOOLEAN |
delete-multiple-replacement | BOOLEAN |
} |
SEQUENCE | { |
obey-stop-codon | BOOLEAN |
} |
CHOICE | { |
aecr | AECR-action |
parse | Parse-action |
add-feature | Apply-feature-action |
remove-feature | Remove-feature-action |
convert-feature | Convert-feature-action |
edit-location | Edit-feature-location-action |
remove-descriptor | Remove-descriptor-action |
autodef | Autodef-action |
removesets | NULL |
trim-junk-from-primer-seq | NULL |
trim-stop-from-complete-cds | NULL |
fix-usa-and-states | NULL |
synchronize-cds-partials | NULL |
adjust-for-consensus-splice | NULL |
fix-pub-caps | Fix-pub-caps-action |
remove-seg-gaps | NULL |
sort-fields | Sort-fields-action |
apply-molinfo-block | Molinfo-block |
fix-caps | Fix-caps-action |
fix-format | Fix-format-action |
fix-spell | NULL |
remove-duplicate-features | Remove-duplicate-feature-action |
remove-lineage-notes | NULL |
remove-xrefs | Remove-xrefs-action |
make-gene-xrefs | Make-gene-xref-action |
make-bold-xrefs | NULL |
fix-author | Author-fix-action |
update-sequences | Update-sequences-action |
add-trans-splicing | NULL |
remove-invalid-ecnumbers | NULL |
create-tsa-ids | Create-TSA-ids-action |
perform-autofix | Autofix-action |
fix-sets | Fix-sets-action |
apply-table | Apply-table-action |
remove-sequences | Remove-sequences-action |
propagate-sequence-technology | NULL |
add-file-descriptors | Add-descriptor-list-action |
propagate-missing-old-name | NULL |
autoapply-structured-comments | NULL |
reorder-structured-comments | NULL |
remove-duplicate-structured-comments | NULL |
lookup-taxonomy | NULL |
lookup-pubs | NULL |
trim-terminal-ns | NULL |
update-replaced-ecnumbers | Update-replaced-ec-numbers-action |
instantiate-protein-titles | NULL |
retranslate-cds | Retranslate-cds-action |
} |
CHOICE | { |
string-constraint | String-constraint |
contains-plural | NULL |
n-or-more-brackets-or-parentheses | INTEGER |
three-numbers | NULL |
underscore | NULL |
prefix-and-numbers | VisibleString |
all-caps | NULL |
unbalanced-paren | NULL |
too-long | INTEGER |
has-term | VisibleString |
} |
SEQUENCE | { |
replace | VisibleString OPTIONAL |
whole-string | BOOLEAN DEFAULT false |
weasel-to-putative | BOOLEAN DEFAULT false |
} |
CHOICE | { |
simple-replace | Simple-replace |
haem-replace | VisibleString |
} |
SEQUENCE | { |
replace-func | Replace-func |
move-to-note | BOOLEAN DEFAULT false |
} |
ENUMERATED | { |
none | 0 |
typo | 1 |
putative-typo | 2 |
quickfix | 3 |
no-organelle-for-prokaryote | 4 |
might-be-nonfunctional | 5 |
database | 6 |
remove-organism-name | 7 |
inappropriate-symbol | 8 |
evolutionary-relationship | 9 |
use-protein | 10 |
hypothetical | 11 |
british | 12 |
description | 13 |
gene | 14 |
} |
SEQUENCE | { |
find | Search-func |
except | Search-func OPTIONAL |
feat-constraint | Constraint-choice-set OPTIONAL |
rule-type | Fix-type DEFAULT none |
replace | Replace-rule OPTIONAL |
description | VisibleString OPTIONAL |
} |