GC-Sequence

Defined in file genome_collection.asn
C++ class: CGC_Sequence


GC-Sequence ::= SEQUENCE {
    -- identifiers are: Local / gpipe-satellite / genbank / refseq
    -- local is merely local name (or maybe with WGS accession??)
    -- others are accession/ver/gi
    --
    -- Main identifier:
    -- we will report the one that matches the context of who asked.
    seq-id Seq-id,
    -- Other known identifiers: Local / gpipe-satellite / genbank / refseq
    seq-id-synonyms SET OF GC-TypedSeqId OPTIONAL,

    -- Various attributes assigned at this level:
    -- biosrc, comments, publications...
    descr Seq-descr OPTIONAL ,

    -- Feature annotation;
    -- Contains Pseudo Autosomal regions on chromosomes and scaffolds in the
    -- following format:
    --   Id = 
    --   Desc (set of Annot-descr)
    --      Name: "pseudo autosomal region"
    --       Region (seq-loc): int (seq-interval)
    --          Id:  
    --            From: 
    --            To : 
    --      Data: locs (set of seq-loc):
    --         List of int (seq-interval):
    --            Id: GI of scaffold
    --              From/to: position on scaffold that belongs to this PAR region.
    --                  
    --
    -- in alt-loci units - contain alignment of this sequence to the primary
    -- unit
    annot SET OF Seq-annot OPTIONAL,

    -- placed: populated both on chromosome and scaffold levels
    -- unlocalized: populated on chromosome level
    sequences SET OF GC-TaggedSequences  OPTIONAL,

    -- locations of ordered scaffolds/components
    structure Delta-ext OPTIONAL,

    -- statistics
    stats GC-SequenceStats OPTIONAL,

    patch-type INTEGER {
        novel(0),
        fix(1),
        -- stopper
        other(255)
    } OPTIONAL,

    -- sequence-role: what role(s) does this sequence have in the assembly
    roles  SET OF GC-SequenceRole OPTIONAL
}