130 lines
4.0 KiB
Groff
130 lines
4.0 KiB
Groff
--$Revision: 182653 $
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--**********************************************************************
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--
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-- NCBI Sequence location and identifier elements
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-- by James Ostell, 1990
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--
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-- Version 3.0 - 1994
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--
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--**********************************************************************
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NCBI-Seqloc DEFINITIONS ::=
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BEGIN
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EXPORTS Seq-id, Seq-loc, Seq-interval, Packed-seqint, Seq-point, Packed-seqpnt,
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Na-strand, Giimport-id;
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IMPORTS Object-id, Int-fuzz, Dbtag, Date FROM NCBI-General
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Id-pat FROM NCBI-Biblio
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Feat-id FROM NCBI-Seqfeat;
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--*** Sequence identifiers ********************************
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--*
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Seq-id ::= CHOICE {
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local Object-id , -- local use
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gibbsq INTEGER , -- Geninfo backbone seqid
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gibbmt INTEGER , -- Geninfo backbone moltype
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giim Giimport-id , -- Geninfo import id
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genbank Textseq-id ,
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embl Textseq-id ,
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pir Textseq-id ,
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swissprot Textseq-id ,
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patent Patent-seq-id ,
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other Textseq-id , -- for historical reasons, 'other' = 'refseq'
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general Dbtag , -- for other databases
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gi INTEGER , -- GenInfo Integrated Database
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ddbj Textseq-id , -- DDBJ
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prf Textseq-id , -- PRF SEQDB
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pdb PDB-seq-id , -- PDB sequence
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tpg Textseq-id , -- Third Party Annot/Seq Genbank
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tpe Textseq-id , -- Third Party Annot/Seq EMBL
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tpd Textseq-id , -- Third Party Annot/Seq DDBJ
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gpipe Textseq-id , -- Internal NCBI genome pipeline processing ID
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named-annot-track Textseq-id -- Internal named annotation tracking ID
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}
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Seq-id-set ::= SET OF Seq-id
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Patent-seq-id ::= SEQUENCE {
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seqid INTEGER , -- number of sequence in patent
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cit Id-pat } -- patent citation
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Textseq-id ::= SEQUENCE {
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name VisibleString OPTIONAL ,
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accession VisibleString OPTIONAL ,
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release VisibleString OPTIONAL ,
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version INTEGER OPTIONAL }
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Giimport-id ::= SEQUENCE {
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id INTEGER , -- the id to use here
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db VisibleString OPTIONAL , -- dbase used in
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release VisibleString OPTIONAL } -- the release
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PDB-seq-id ::= SEQUENCE {
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mol PDB-mol-id , -- the molecule name
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chain INTEGER DEFAULT 32 , -- a single ASCII character, chain id
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rel Date OPTIONAL } -- release date, month and year
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PDB-mol-id ::= VisibleString -- name of mol, 4 chars
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--*** Sequence locations **********************************
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--*
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Seq-loc ::= CHOICE {
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null NULL , -- not placed
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empty Seq-id , -- to NULL one Seq-id in a collection
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whole Seq-id , -- whole sequence
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int Seq-interval , -- from to
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packed-int Packed-seqint ,
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pnt Seq-point ,
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packed-pnt Packed-seqpnt ,
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mix Seq-loc-mix ,
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equiv Seq-loc-equiv , -- equivalent sets of locations
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bond Seq-bond ,
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feat Feat-id } -- indirect, through a Seq-feat
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Seq-interval ::= SEQUENCE {
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from INTEGER ,
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to INTEGER ,
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strand Na-strand OPTIONAL ,
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id Seq-id , -- WARNING: this used to be optional
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fuzz-from Int-fuzz OPTIONAL ,
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fuzz-to Int-fuzz OPTIONAL }
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Packed-seqint ::= SEQUENCE OF Seq-interval
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Seq-point ::= SEQUENCE {
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point INTEGER ,
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strand Na-strand OPTIONAL ,
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id Seq-id , -- WARNING: this used to be optional
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fuzz Int-fuzz OPTIONAL }
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Packed-seqpnt ::= SEQUENCE {
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strand Na-strand OPTIONAL ,
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id Seq-id ,
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fuzz Int-fuzz OPTIONAL ,
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points SEQUENCE OF INTEGER }
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Na-strand ::= ENUMERATED { -- strand of nucleic acid
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unknown (0) ,
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plus (1) ,
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minus (2) ,
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both (3) , -- in forward orientation
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both-rev (4) , -- in reverse orientation
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other (255) }
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Seq-bond ::= SEQUENCE { -- bond between residues
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a Seq-point , -- connection to a least one residue
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b Seq-point OPTIONAL } -- other end may not be available
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Seq-loc-mix ::= SEQUENCE OF Seq-loc -- this will hold anything
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Seq-loc-equiv ::= SET OF Seq-loc -- for a set of equivalent locations
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END
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