ASN.1 Type Definitions for Module NCBI-Sequence

Top-level module index.

Colors and Styles Used


Type Bioseq

Uses

Seq-annot Seq-descr Seq-id Seq-inst

Is Used By

Blast4-get-sequences-reply Blast4-subject Blast4-value Cdd ID2S-Chunk-Data MSBioseq SeqEdit-Cmd-AttachSeq Seq-entry Variation Bioseq ::=
SEQUENCE {
id SET OF Seq-id
descr Seq-descr OPTIONAL
inst Seq-inst
annot SET OF Seq-annot OPTIONAL
}  


Type Seq-descr

Uses

Seqdesc

Is Used By

Bioseq Bioseq-set GC-AssemblyDesc GC-Genome GC-Sequence ID2S-Chunk-Data SeqEdit-Cmd-AddDescr SeqEdit-Cmd-SetDescr Seq-descr ::= SET OF Seqdesc

Type Seqdesc

Uses

BioSource Date Dbtag EMBL-block GB-block GIBB-method GIBB-mod GIBB-mol Heterogen ModelEvidenceSupport MolInfo Numbering Org-ref PDB-block PIR-block PRF-block Pubdesc SP-block User-object

Is Used By

Seq-descr SeqEdit-Cmd-AddDesc SeqEdit-Cmd-RemoveDesc Seqdesc ::=
CHOICE {
mol-type GIBB-mol
modif SET OF GIBB-mod
method GIBB-method
name VisibleString
title VisibleString
org Org-ref
comment VisibleString
num Numbering
maploc Dbtag
pir PIR-block
genbank GB-block
pub Pubdesc
region VisibleString
user User-object
sp SP-block
dbxref Dbtag
embl EMBL-block
create-date Date
update-date Date
prf PRF-block
pdb PDB-block
het Heterogen
source BioSource
molinfo MolInfo
modelev ModelEvidenceSupport
}  


Type MolInfo

Is Used By

Seqdesc MolInfo ::=
SEQUENCE {
biomol
INTEGER {
unknown 0
genomic 1
pre-RNA 2
mRNA 3
rRNA 4
tRNA 5
snRNA 6
scRNA 7
peptide 8
other-genetic 9
genomic-mRNA 10
cRNA 11
snoRNA 12
transcribed-RNA 13
ncRNA 14
tmRNA 15
other 255
}  
DEFAULT unknown
tech
INTEGER {
unknown 0
standard 1
est 2
sts 3
survey 4
genemap 5
physmap 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 255
}  
DEFAULT unknown
techexp VisibleString OPTIONAL
completeness
INTEGER {
unknown 0
complete 1
partial 2
no-left 3
no-right 4
no-ends 5
has-left 6
has-right 7
other 255
}  
DEFAULT unknown
gbmoltype VisibleString OPTIONAL
}  


Type GIBB-mol

Is Used By

Seqdesc GIBB-mol ::=
ENUMERATED {
unknown 0
genomic 1
pre-mRNA 2
mRNA 3
rRNA 4
tRNA 5
snRNA 6
scRNA 7
peptide 8
other-genetic 9
genomic-mRNA 10
other 255
}  


Type GIBB-mod

Is Used By

Seqdesc GIBB-mod ::=
ENUMERATED {
dna 0
rna 1
extrachrom 2
plasmid 3
mitochondrial 4
chloroplast 5
kinetoplast 6
cyanelle 7
synthetic 8
recombinant 9
partial 10
complete 11
mutagen 12
natmut 13
transposon 14
insertion-seq 15
no-left 16
no-right 17
macronuclear 18
proviral 19
est 20
sts 21
survey 22
chromoplast 23
genemap 24
restmap 25
physmap 26
other 255
}  


Type GIBB-method

Is Used By

Seqdesc GIBB-method ::=
ENUMERATED {
concept-trans 1
seq-pept 2
both 3
seq-pept-overlap 4
seq-pept-homol 5
concept-trans-a 6
other 255
}  


Type Numbering

Uses

Num-cont Num-enum Num-real Num-ref

Is Used By

Pubdesc Seqdesc SeqFeatData Numbering ::=
CHOICE {
cont Num-cont
enum Num-enum
ref Num-ref
real Num-real
}  


Type Num-cont

Is Used By

Numbering Num-cont ::=
SEQUENCE {
refnum INTEGER DEFAULT 1
has-zero BOOLEAN DEFAULT false
ascending BOOLEAN DEFAULT true
}  


Type Num-enum

Is Used By

Numbering Num-enum ::=
SEQUENCE {
num INTEGER
names SEQUENCE OF VisibleString
}  


Type Num-ref

Uses

Seq-align

Is Used By

Numbering Num-ref ::=
SEQUENCE {
type
ENUMERATED {
not-set 0
sources 1
aligns 2
}  
aligns Seq-align OPTIONAL
}  


Type Num-real

Is Used By

Numbering Num-real ::=
SEQUENCE {
a REAL
b REAL
units VisibleString OPTIONAL
}  


Type Pubdesc

Uses

Numbering Pub-equiv StringStore

Is Used By

Annotdesc Projdesc Seqdesc SeqFeatData Pubdesc ::=
SEQUENCE {
pub Pub-equiv
name VisibleString OPTIONAL
fig VisibleString OPTIONAL
num Numbering OPTIONAL
numexc BOOLEAN OPTIONAL
poly-a BOOLEAN OPTIONAL
maploc VisibleString OPTIONAL
seq-raw StringStore OPTIONAL
align-group INTEGER OPTIONAL
comment VisibleString OPTIONAL
reftype
INTEGER {
seq 0
sites 1
feats 2
no-target 3
}  
DEFAULT seq
}  


Type Heterogen

Is Used By

Seqdesc SeqFeatData Heterogen ::= VisibleString

Type Seq-inst

Uses

Int-fuzz Seq-data Seq-ext Seq-hist

Is Used By

Bioseq SeqEdit-Cmd-ChangeSeqAttr Seq-inst ::=
SEQUENCE {
repr
ENUMERATED {
not-set 0
virtual 1
raw 2
seg 3
const 4
ref 5
consen 6
map 7
delta 8
other 255
}  
mol
ENUMERATED {
not-set 0
dna 1
rna 2
aa 3
na 4
other 255
}  
length INTEGER OPTIONAL
fuzz Int-fuzz OPTIONAL
topology
ENUMERATED {
not-set 0
linear 1
circular 2
tandem 3
other 255
}  
DEFAULT linear
strand
ENUMERATED {
not-set 0
ss 1
ds 2
mixed 3
other 255
}  
OPTIONAL
seq-data Seq-data OPTIONAL
ext Seq-ext OPTIONAL
hist Seq-hist OPTIONAL
}  


Type Seq-ext

Uses

Delta-ext Map-ext Ref-ext Seg-ext

Is Used By

SeqEdit-Cmd-ChangeSeqAttr Seq-inst Seq-ext ::=
CHOICE {
seg Seg-ext
ref Ref-ext
map Map-ext
delta Delta-ext
}  


Type Seg-ext

Uses

Seq-loc

Is Used By

Seq-ext Seg-ext ::= SEQUENCE OF Seq-loc

Type Ref-ext

Uses

Seq-loc

Is Used By

Seq-ext Ref-ext ::= Seq-loc

Type Map-ext

Uses

Seq-feat

Is Used By

Seq-ext Map-ext ::= SEQUENCE OF Seq-feat

Type Delta-ext

Uses

Delta-seq

Is Used By

GC-Sequence Seq-ext Delta-ext ::= SEQUENCE OF Delta-seq

Type Delta-seq

Uses

Seq-literal Seq-loc

Is Used By

Delta-ext Delta-seq ::=
CHOICE {
loc Seq-loc
literal Seq-literal
}  


Type Seq-literal

Uses

Int-fuzz Seq-data

Is Used By

Delta-item Delta-seq ID2S-Sequence-Piece VariantPlacement Seq-literal ::=
SEQUENCE {
length INTEGER
fuzz Int-fuzz OPTIONAL
seq-data Seq-data OPTIONAL
}  


Type Seq-hist

Uses

Date Seq-align Seq-hist-rec

Is Used By

ID1Seq-hist SeqEdit-Cmd-ChangeSeqAttr Seq-inst Seq-hist ::=
SEQUENCE {
assembly SET OF Seq-align OPTIONAL
replaces Seq-hist-rec OPTIONAL
replaced-by Seq-hist-rec OPTIONAL
deleted
CHOICE {
bool BOOLEAN
date Date
}  
OPTIONAL
}  


Type Seq-hist-rec

Uses

Date Seq-id

Is Used By

Seq-hist Seq-hist-rec ::=
SEQUENCE {
date Date OPTIONAL
ids SET OF Seq-id
}  


Type Seq-data

Uses

IUPACaa IUPACna NCBI2na NCBI4na NCBI8aa NCBI8na NCBIeaa NCBIpaa NCBIpna NCBIstdaa Seq-gap

Is Used By

Blast4-seq-part-data SeqEdit-Cmd-ChangeSeqAttr Seq-inst Seq-literal Seq-data ::=
CHOICE {
iupacna IUPACna
iupacaa IUPACaa
ncbi2na NCBI2na
ncbi4na NCBI4na
ncbi8na NCBI8na
ncbipna NCBIpna
ncbi8aa NCBI8aa
ncbieaa NCBIeaa
ncbipaa NCBIpaa
ncbistdaa NCBIstdaa
gap Seq-gap
}  


Type Seq-gap

Uses

Linkage-evidence

Is Used By

Seq-data Seq-gap ::=
SEQUENCE {
type
INTEGER {
unknown 0
fragment 1
clone 2
short-arm 3
heterochromatin 4
centromere 5
telomere 6
repeat 7
contig 8
scaffold 9
other 255
}  
linkage
INTEGER {
unlinked 0
linked 1
other 255
}  
OPTIONAL
linkage-evidence SET OF Linkage-evidence OPTIONAL
}  


Type Linkage-evidence

Is Used By

Seq-gap Linkage-evidence ::=
SEQUENCE {
type
INTEGER {
paired-ends 0
align-genus 1
align-xgenus 2
align-trnscpt 3
within-clone 4
clone-contig 5
map 6
strobe 7
unspecified 8
pcr 9
other 255
}  
}  


Type IUPACna

Uses

StringStore

Is Used By

Seq-data IUPACna ::= StringStore

Type IUPACaa

Uses

StringStore

Is Used By

Seq-data IUPACaa ::= StringStore

Type NCBI2na

Is Used By

Seq-data NCBI2na ::= OCTET_STRING

Type NCBI4na

Is Used By

Seq-data NCBI4na ::= OCTET_STRING

Type NCBI8na

Is Used By

Seq-data NCBI8na ::= OCTET_STRING

Type NCBIpna

Is Used By

Seq-data NCBIpna ::= OCTET_STRING

Type NCBI8aa

Is Used By

Seq-data NCBI8aa ::= OCTET_STRING

Type NCBIeaa

Uses

StringStore

Is Used By

Seq-data NCBIeaa ::= StringStore

Type NCBIpaa

Is Used By

Seq-data NCBIpaa ::= OCTET_STRING

Type NCBIstdaa

Is Used By

Seq-data NCBIstdaa ::= OCTET_STRING

Type Textannot-id

Is Used By

Annot-id Textannot-id ::=
SEQUENCE {
name VisibleString OPTIONAL
accession VisibleString OPTIONAL
release VisibleString OPTIONAL
version INTEGER OPTIONAL
}  


Type Annot-id

Uses

Dbtag Object-id Textannot-id

Is Used By

Seq-annot Annot-id ::=
CHOICE {
local Object-id
ncbi INTEGER
general Dbtag
other Textannot-id
}  


Type Annot-descr

Uses

Annotdesc

Is Used By

Seq-annot SeqEdit-Cmd-AddAnnot Annot-descr ::= SET OF Annotdesc

Type Annotdesc

Uses

Align-def Date Pubdesc Seq-id Seq-loc User-object

Is Used By

Annot-descr Annotdesc ::=
CHOICE {
name VisibleString
title VisibleString
comment VisibleString
pub Pubdesc
user User-object
create-date Date
update-date Date
src Seq-id
align Align-def
region Seq-loc
}  


Type Align-def

Uses

Seq-id

Is Used By

Annotdesc Align-def ::=
SEQUENCE {
align-type
INTEGER {
ref 1
alt 2
blocks 3
other 255
}  
ids SET OF Seq-id OPTIONAL
}  


Type Seq-annot

Uses

Annot-descr Annot-id Seq-align Seq-feat Seq-graph Seq-id Seq-loc Seq-table

Is Used By

Bioseq Bioseq-set Biostruc-align Biostruc-align-seq Biostruc-seqs Bundle-seqs-aligns Cdd Domain-parent GC-AssemblyDesc GC-Sequence ID2S-Chunk-Data Project-item SeqEdit-Cmd-AttachAnnot Seq-submit Update-align Seq-annot ::=
SEQUENCE {
id SET OF Annot-id OPTIONAL
db
INTEGER {
genbank 1
embl 2
ddbj 3
pir 4
sp 5
bbone 6
pdb 7
other 255
}  
OPTIONAL
name VisibleString OPTIONAL
desc Annot-descr OPTIONAL
data
CHOICE {
ftable SET OF Seq-feat
align SET OF Seq-align
graph SET OF Seq-graph
ids SET OF Seq-id
locs SET OF Seq-loc
seq-table Seq-table
}  
}  


Top-level module index.