all.asn

ncbi源码

    dim INTEGER OPTIONAL ,     -- dimensionality
    score SET OF Score OPTIONAL ,   -- for whole alignment
    segs CHOICE {                   -- alignment data
        dendiag SEQUENCE OF Dense-diag ,
        denseg Dense-seg ,
        std SEQUENCE OF Std-seg ,
	packed Packed-seg ,
	disc Seq-align-set } ,
    bounds SET OF Seq-loc OPTIONAL }  -- regions of sequence over which align
                                      --  was computed

Dense-diag ::= SEQUENCE {         -- for (multiway) diagonals
    dim INTEGER DEFAULT 2 ,    -- dimensionality
    ids SEQUENCE OF Seq-id ,   -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order
    len INTEGER ,                 -- len of aligned segments
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SET OF Score OPTIONAL }

    -- Dense-seg: the densist packing for sequence alignments only.
    --            a start of -1 indicates a gap for that sequence of
    --            length lens.
    --
    -- id=100  AAGGCCTTTTAGAGATGATGATGATGATGA
    -- id=200  AAGGCCTTTTAG.......GATGATGATGA
    -- id=300  ....CCTTTTAGAGATGATGAT....ATGA
    --
    -- dim = 3, numseg = 6, ids = { 100, 200, 300 }
    -- starts = { 0,0,-1, 4,4,0, 12,-1,8, 19,12,15, 22,15,-1, 26,19,18 }
    -- lens = { 4, 8, 7, 3, 4, 4 }
    --

Dense-seg ::= SEQUENCE {          -- for (multiway) global or partial alignments
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    numseg INTEGER ,              -- number of segments here
    ids SEQUENCE OF Seq-id ,      -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order within segs
    lens SEQUENCE OF INTEGER ,    -- lengths in ids order within segs
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SEQUENCE OF Score OPTIONAL }  -- score for each seg

Packed-seg ::= SEQUENCE {         -- for (multiway) global or partial alignments
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    numseg INTEGER ,              -- number of segments here
    ids SEQUENCE OF Seq-id ,      -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order for whole alignment
    present OCTET STRING ,        -- Boolean if each sequence present or absent in
                                  --   each segment
    lens SEQUENCE OF INTEGER ,    -- length of each segment
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SEQUENCE OF Score OPTIONAL }  -- score for each segment

Std-seg ::= SEQUENCE {
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    ids SEQUENCE OF Seq-id OPTIONAL ,
    loc SEQUENCE OF Seq-loc ,
    scores SET OF Score OPTIONAL }

-- use of Score is discouraged for external ASN.1 specifications
Score ::= SEQUENCE {
    id Object-id OPTIONAL ,
    value CHOICE {
        real REAL ,
        int INTEGER  } }

-- use of Score-set is encouraged for external ASN.1 specifications
Score-set ::= SET OF Score

END 

--$Revision: 1000.1 $
--*********************************************************************
--
-- 1990 - J.Ostell
-- Version 3.0 - June 1994
--
--*********************************************************************
--*********************************************************************
--
--  EMBL specific data
--  This block of specifications was developed by Reiner Fuchs of EMBL
--  Updated by J.Ostell, 1994
--
--*********************************************************************

EMBL-General DEFINITIONS ::=
BEGIN

EXPORTS EMBL-dbname, EMBL-xref, EMBL-block;

IMPORTS Date, Object-id FROM NCBI-General;

EMBL-dbname ::= CHOICE {
    code ENUMERATED {
        embl(0),
        genbank(1),
        ddbj(2),
        geninfo(3),
        medline(4),
        swissprot(5),
        pir(6),
        pdb(7),
        epd(8),
        ecd(9),
        tfd(10),
        flybase(11),
        prosite(12),
        enzyme(13),
        mim(14),
        ecoseq(15),
        hiv(16) ,
        other (255) } ,
    name    VisibleString }

EMBL-xref ::= SEQUENCE {
    dbname EMBL-dbname,
    id SEQUENCE OF Object-id }

EMBL-block ::= SEQUENCE {
    class ENUMERATED {
        not-set(0),
        standard(1),
        unannotated(2),
        other(255) } DEFAULT standard,
    div ENUMERATED {
        fun(0),
        inv(1),
        mam(2),
        org(3),
        phg(4),
        pln(5),
        pri(6),
        pro(7),
        rod(8),
        syn(9),
        una(10),
        vrl(11),
        vrt(12),
        pat(13),
        est(14),
        sts(15),
        other (255) } OPTIONAL,
    creation-date Date,
    update-date Date,
    extra-acc SEQUENCE OF VisibleString OPTIONAL,
    keywords SEQUENCE OF VisibleString OPTIONAL,
    xref SEQUENCE OF EMBL-xref OPTIONAL }

END

--*********************************************************************
--
--  SWISSPROT specific data
--  This block of specifications was developed by Mark Cavanaugh of
--      NCBI working with Amos Bairoch of SWISSPROT
--
--*********************************************************************

SP-General DEFINITIONS ::=
BEGIN

EXPORTS SP-block;

IMPORTS Date, Dbtag FROM NCBI-General
        Seq-id FROM NCBI-Seqloc;

SP-block ::= SEQUENCE {         -- SWISSPROT specific descriptions
    class ENUMERATED {
        not-set (0) ,
        standard (1) ,      -- conforms to all SWISSPROT checks
        prelim (2) ,        -- only seq and biblio checked
        other (255) } ,
    extra-acc SET OF VisibleString OPTIONAL ,  -- old SWISSPROT ids
    imeth BOOLEAN DEFAULT FALSE ,  -- seq known to start with Met
    plasnm SET OF VisibleString OPTIONAL,  -- plasmid names carrying gene
    seqref SET OF Seq-id OPTIONAL,         -- xref to other sequences
    dbref SET OF Dbtag OPTIONAL ,          -- xref to non-sequence dbases
    keywords SET OF VisibleString OPTIONAL , -- keywords
    created Date OPTIONAL ,         -- creation date
    sequpd Date OPTIONAL ,          -- sequence update
    annotupd Date OPTIONAL }        -- annotation update

END

--*********************************************************************
--
--  PIR specific data
--  This block of specifications was developed by Jim Ostell of
--      NCBI
--
--*********************************************************************

PIR-General DEFINITIONS ::=
BEGIN

EXPORTS PIR-block;

IMPORTS Seq-id FROM NCBI-Seqloc;

PIR-block ::= SEQUENCE {          -- PIR specific descriptions
    had-punct BOOLEAN OPTIONAL ,      -- had punctuation in sequence ?
    host VisibleString OPTIONAL ,
    source VisibleString OPTIONAL ,     -- source line
    summary VisibleString OPTIONAL ,
    genetic VisibleString OPTIONAL ,
    includes VisibleString OPTIONAL ,
    placement VisibleString OPTIONAL ,
    superfamily VisibleString OPTIONAL ,
    keywords SEQUENCE OF VisibleString OPTIONAL ,
    cross-reference VisibleString OPTIONAL ,
    date VisibleString OPTIONAL ,
    seq-raw VisibleString OPTIONAL ,  -- seq with punctuation
    seqref SET OF Seq-id OPTIONAL }         -- xref to other sequences

END

--*********************************************************************
--
--  GenBank specific data
--  This block of specifications was developed by Jim Ostell of
--      NCBI
--
--*********************************************************************

GenBank-General DEFINITIONS ::=
BEGIN

EXPORTS GB-block;

IMPORTS Date FROM NCBI-General;

GB-block ::= SEQUENCE {          -- GenBank specific descriptions
    extra-accessions SEQUENCE OF VisibleString OPTIONAL ,
    source VisibleString OPTIONAL ,     -- source line
    keywords SEQUENCE OF VisibleString OPTIONAL ,
    origin VisibleString OPTIONAL,
    date VisibleString OPTIONAL ,       -- OBSOLETE old form Entry Date
    entry-date Date OPTIONAL ,          -- replaces date
    div VisibleString OPTIONAL ,        -- GenBank division
    taxonomy VisibleString OPTIONAL }   -- continuation line of organism

END

--**********************************************************************
-- PRF specific definition
--    PRF is a protein sequence database crated and maintained by
--    Protein Research Foundation, Minoo-city, Osaka, Japan.
--
--    Written by A.Ogiwara, Inst.Chem.Res. (Dr.Kanehisa's Lab),
--            Kyoto Univ., Japan
--
--**********************************************************************

PRF-General DEFINITIONS ::=
BEGIN

EXPORTS PRF-block;

PRF-block ::= SEQUENCE {
      extra-src       PRF-ExtraSrc OPTIONAL,
      keywords        SEQUENCE OF VisibleString OPTIONAL
}

PRF-ExtraSrc ::= SEQUENCE {
      host    VisibleString OPTIONAL,
      part    VisibleString OPTIONAL,
      state   VisibleString OPTIONAL,
      strain  VisibleString OPTIONAL,
      taxon   VisibleString OPTIONAL
}

END

--*********************************************************************
--
--  PDB specific data
--  This block of specifications was developed by Jim Ostell and
--      Steve Bryant of NCBI
--
--*********************************************************************

PDB-General DEFINITIONS ::=
BEGIN

EXPORTS PDB-block;

IMPORTS Date FROM NCBI-General;

PDB-block ::= SEQUENCE {          -- PDB specific descriptions
    deposition Date ,         -- deposition date  month,year
    class VisibleString ,
    compound SEQUENCE OF VisibleString ,
    source SEQUENCE OF VisibleString ,
    exp-method VisibleString OPTIONAL ,  -- present if NOT X-ray diffraction
    replace PDB-replace OPTIONAL } -- replacement history

PDB-replace ::= SEQUENCE {
    date Date ,
    ids SEQUENCE OF VisibleString }   -- entry ids replace by this one

END

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

NCBI-Seqfeat DEFINITIONS ::=
BEGIN

EXPORTS Seq-feat, Feat-id, Genetic-code;

IMPORTS Gene-ref FROM NCBI-Gene
        Prot-ref FROM NCBI-Protein
        Org-ref FROM NCBI-Organism
        BioSource FROM NCBI-BioSource
        RNA-ref FROM NCBI-RNA
        Seq-loc, Giimport-id FROM NCBI-Seqloc
        Pubdesc, Numbering, Heterogen FROM NCBI-Sequence
        Rsite-ref FROM NCBI-Rsite
        Txinit FROM NCBI-TxInit
        Pub-set FROM NCBI-Pub
        Object-id, Dbtag, User-object FROM NCBI-General;

--*** Feature identifiers ********************************
--*

Feat-id ::= CHOICE {
    gibb INTEGER ,            -- geninfo backbone
    giim Giimport-id ,        -- geninfo import
    local Object-id ,         -- for local software use
    general Dbtag }           -- for use by various databases

--*** Seq-feat *******************************************
--*  sequence feature generalization

Seq-feat ::= SEQUENCE {
    id Feat-id OPTIONAL ,
    data SeqFeatData ,           -- the specific data
    partial BOOLEAN OPTIONAL ,    -- incomplete in some way?
    except BOOLEAN OPTIONAL ,     -- something funny about this?
    comment VisibleString OPTIONAL ,
    product Seq-loc OPTIONAL ,    -- product of process
    location Seq-loc ,            -- feature made from
    qual SEQUENCE OF Gb-qual OPTIONAL ,  -- qualifiers
    title VisibleString OPTIONAL ,   -- for user defined label
    ext User-object OPTIONAL ,    -- user defined structure extension
    cit Pub-set OPTIONAL ,        -- citations for this feature
    exp-ev ENUMERATED {           -- evidence for existence of feature
        experimental (1) ,        -- any reasonable experimental check
        not-experimental (2) } OPTIONAL , -- similarity, pattern, etc
    xref SET OF SeqFeatXref OPTIONAL ,   -- cite other relevant features
	dbxref SET OF Dbtag OPTIONAL ,  -- support for xref to other databases
    pseudo BOOLEAN OPTIONAL ,     -- annotated on pseudogene?
    except-text VisibleString OPTIONAL } -- explain if except=TRUE

SeqFeatData ::= CHOICE {
    gene Gene-ref ,
    org Org-ref ,
    cdregion Cdregion ,
    prot Prot-ref ,
    rna RNA-ref ,
    pub Pubdesc ,              -- publication applies to this seq 
    seq Seq-loc ,              -- to annotate origin from another seq
    imp Imp-feat ,
    region VisibleString,      -- named region (globin locus)
    comment NULL ,             -- just a comment
    bond ENUMERATED {
        disulfide (1) ,
        thiolester (2) ,
        xlink (3) ,
        thioether (4) ,
        other (255) } ,