seq.asn

ncbi源码

--$Revision: 1000.1 $
--**********************************************************************
--
--  NCBI Sequence elements
--  by James Ostell, 1990
--  Version 3.0 - June 1994
--
--**********************************************************************

NCBI-Sequence DEFINITIONS ::=
BEGIN

EXPORTS Annotdesc, Bioseq, GIBB-mol, Heterogen, Numbering, Pubdesc,
        Seq-annot, Seq-descr, Seq-hist, Seq-literal, Seqdesc;

IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
        Seq-align FROM NCBI-Seqalign
        Seq-feat FROM NCBI-Seqfeat
        Seq-graph FROM NCBI-Seqres
        Pub-equiv FROM NCBI-Pub
        Org-ref FROM NCBI-Organism
        BioSource FROM NCBI-BioSource
        Seq-id, Seq-loc FROM NCBI-Seqloc
        GB-block FROM GenBank-General
        PIR-block FROM PIR-General
        EMBL-block FROM EMBL-General
        SP-block FROM SP-General
        PRF-block FROM PRF-General
        PDB-block FROM PDB-General;

--*** Sequence ********************************
--*

Bioseq ::= SEQUENCE {
    id SET OF Seq-id ,            -- equivalent identifiers
    descr Seq-descr OPTIONAL , -- descriptors
    inst Seq-inst ,            -- the sequence data
    annot SET OF Seq-annot OPTIONAL }

--*** Descriptors *****************************
--*

Seq-descr ::= SET OF Seqdesc

Seqdesc ::= CHOICE {
    mol-type GIBB-mol ,          -- type of molecule
    modif SET OF GIBB-mod ,             -- modifiers
    method GIBB-method ,         -- sequencing method
    name VisibleString ,         -- a name for this sequence
    title VisibleString ,        -- a title for this sequence
    org Org-ref ,                -- if all from one organism
    comment VisibleString ,      -- a more extensive comment
    num Numbering ,              -- a numbering system
    maploc Dbtag ,               -- map location of this sequence
    pir PIR-block ,              -- PIR specific info
    genbank GB-block ,           -- GenBank specific info
    pub Pubdesc ,                -- a reference to the publication
    region VisibleString ,       -- overall region (globin locus)
    user User-object ,           -- user defined object
    sp SP-block ,                -- SWISSPROT specific info
    dbxref Dbtag ,               -- xref to other databases
    embl EMBL-block ,            -- EMBL specific information
    create-date Date ,           -- date entry first created/released
    update-date Date ,           -- date of last update
    prf PRF-block ,              -- PRF specific information
    pdb PDB-block ,              -- PDB specific information
    het Heterogen ,              -- cofactor, etc associated but not bound
    source BioSource ,           -- source of materials, includes Org-ref
    molinfo MolInfo }            -- info on the molecule and techniques

--******* NOTE:
--*       mol-type, modif, method, and org are consolidated and expanded
--*       in Org-ref, BioSource, and MolInfo in this specification. They
--*       will be removed in later specifications. Do not use them in the
--*       the future. Instead expect the new structures.
--*
--***************************

--********************************************************************
--
-- MolInfo gives information on the
-- classification of the type and quality of the sequence
--
-- WARNING: this will replace GIBB-mol, GIBB-mod, GIBB-method
--
--********************************************************************

MolInfo ::= SEQUENCE {
    biomol INTEGER {
        unknown (0) ,
        genomic (1) ,
        pre-RNA (2) ,              -- precursor RNA of any sort really 
        mRNA (3) ,
        rRNA (4) ,
        tRNA (5) ,
        snRNA (6) ,
        scRNA (7) ,
        peptide (8) ,
        other-genetic (9) ,      -- other genetic material
        genomic-mRNA (10) ,      -- reported a mix of genomic and cdna sequence
        cRNA (11) ,              -- viral RNA genome copy intermediate
        snoRNA (12) ,            -- small nucleolar RNA
        transcribed-RNA (13) ,   -- transcribed RNA other than existing classes
        other (255) } DEFAULT unknown ,
    tech INTEGER {
        unknown (0) ,
        standard (1) ,          -- standard sequencing
        est (2) ,               -- Expressed Sequence Tag
        sts (3) ,               -- Sequence Tagged Site
        survey (4) ,            -- one-pass genomic sequence
        genemap (5) ,           -- from genetic mapping techniques
        physmap (6) ,           -- from physical mapping techniques
        derived (7) ,           -- derived from other data, not a primary entity
        concept-trans (8) ,     -- conceptual translation
        seq-pept (9) ,          -- peptide was sequenced
        both (10) ,             -- concept transl. w/ partial pept. seq.
        seq-pept-overlap (11) , -- sequenced peptide, ordered by overlap
        seq-pept-homol (12) ,   -- sequenced peptide, ordered by homology
        concept-trans-a (13) ,  -- conceptual transl. supplied by author
        htgs-1 (14) ,           -- unordered High Throughput sequence contig
        htgs-2 (15) ,           -- ordered High Throughput sequence contig
        htgs-3 (16) ,           -- finished High Throughput sequence
        fli-cdna (17) ,         -- full length insert cDNA
        htgs-0 (18) ,           -- single genomic reads for coordination
        htc (19) ,              -- high throughput cDNA
        wgs (20) ,              -- whole genome shotgun sequencing
        other (255) }           -- use Source.techexp
               DEFAULT unknown ,
    techexp VisibleString OPTIONAL ,   -- explanation if tech not enough
    --
    -- Completeness is not indicated in most records.  For genomes, assume
    -- the sequences are incomplete unless specifically marked as complete.
    -- For mRNAs, assume the ends are not known exactly unless marked as
    -- having the left or right end.
    --
    completeness INTEGER {
      unknown (0) ,
      complete (1) ,                   -- complete biological entity
      partial (2) ,                    -- partial but no details given
      no-left (3) ,                    -- missing 5' or NH3 end
      no-right (4) ,                   -- missing 3' or COOH end
      no-ends (5) ,                    -- missing both ends
      has-left (6) ,                   -- 5' or NH3 end present
      has-right (7) ,                  -- 3' or COOH end present
      other (255) } DEFAULT unknown }


GIBB-mol ::= ENUMERATED {       -- type of molecule represented
    unknown (0) ,
    genomic (1) ,
    pre-mRNA (2) ,              -- precursor RNA of any sort really 
    mRNA (3) ,
    rRNA (4) ,
    tRNA (5) ,
    snRNA (6) ,
    scRNA (7) ,
    peptide (8) ,
    other-genetic (9) ,      -- other genetic material
    genomic-mRNA (10) ,      -- reported a mix of genomic and cdna sequence
    other (255) }
    
GIBB-mod ::= ENUMERATED {        -- GenInfo Backbone modifiers
    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) ,    -- subject of mutagenesis ?
    natmut (13) ,     -- natural mutant ?
    transposon (14) ,
    insertion-seq (15) ,
    no-left (16) ,    -- missing left end (5' for na, NH2 for aa)
    no-right (17) ,   -- missing right end (3' or COOH)
    macronuclear (18) ,
    proviral (19) ,
    est (20) ,        -- expressed sequence tag
    sts (21) ,        -- sequence tagged site
    survey (22) ,     -- one pass survey sequence
    chromoplast (23) ,
    genemap (24) ,    -- is a genetic map
    restmap (25) ,    -- is an ordered restriction map
    physmap (26) ,    -- is a physical map (not ordered restriction map)
    other (255) }

GIBB-method ::= ENUMERATED {        -- sequencing methods
    concept-trans (1) ,    -- conceptual translation
    seq-pept (2) ,         -- peptide was sequenced
    both (3) ,             -- concept transl. w/ partial pept. seq.
    seq-pept-overlap (4) , -- sequenced peptide, ordered by overlap
    seq-pept-homol (5) ,   -- sequenced peptide, ordered by homology
    concept-trans-a (6) ,  -- conceptual transl. supplied by author
    other (255) }
    
Numbering ::= CHOICE {           -- any display numbering system
    cont Num-cont ,              -- continuous numbering
    enum Num-enum ,              -- enumerated names for residues
    ref Num-ref ,                -- by reference to another sequence
    real Num-real }              -- supports mapping to a float system
    
Num-cont ::= SEQUENCE {          -- continuous display numbering system
    refnum INTEGER DEFAULT 1,         -- number assigned to first residue
    has-zero BOOLEAN DEFAULT FALSE ,  -- 0 used?