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
}