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72 lines
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2.7 KiB
HTML
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<h3>GC-Sequence</h3><pre>Defined in file <a href="genome_collection.asn.html">genome_collection.asn</a>
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C++ class: <a href="../doxyhtml/classCGC__Sequence.html">CGC_Sequence</a>
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GC-Sequence ::= SEQUENCE {
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-- identifiers are: Local / gpipe-satellite / genbank / refseq
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-- local is merely local name (or maybe with WGS accession??)
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-- others are accession/ver/gi
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--
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-- Main identifier:
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-- we will report the one that matches the context of who asked.
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seq-id <a href="Seq-id.html">Seq-id</a>,
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-- Other known identifiers: Local / gpipe-satellite / genbank / refseq
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seq-id-synonyms SET OF <a href="GC-TypedSeqId.html">GC-TypedSeqId</a> OPTIONAL,
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-- Various attributes assigned at this level:
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-- biosrc, comments, publications...
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descr <a href="Seq-descr.html">Seq-descr</a> OPTIONAL ,
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-- Feature annotation;
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-- Contains Pseudo Autosomal regions on chromosomes and scaffolds in the
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-- following format:
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-- Id = <ID of PAR (ex:"PAR#1")>
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-- Desc (set of <a href="Annot-descr.html">Annot-descr</a>)
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-- Name: "pseudo autosomal region"
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-- Region (seq-loc): int (seq-interval)
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-- Id: <GI of chromosome>
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-- From: <start-position of region>
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-- To : <end-position of region>
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-- Data: locs (set of seq-loc):
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-- List of int (seq-interval):
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-- Id: GI of scaffold
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-- From/to: position on scaffold that belongs to this PAR region.
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-- <and repeat this for additional scaffolds on same PAR region>
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--
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-- in alt-loci units - contain alignment of this sequence to the primary
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-- unit
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annot SET OF <a href="Seq-annot.html">Seq-annot</a> OPTIONAL,
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-- placed: populated both on chromosome and scaffold levels
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-- unlocalized: populated on chromosome level
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sequences SET OF <a href="GC-TaggedSequences.html">GC-TaggedSequences</a> OPTIONAL,
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-- locations of ordered scaffolds/components
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structure <a href="Delta-ext.html">Delta-ext</a> OPTIONAL,
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-- statistics
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stats <a href="GC-SequenceStats.html">GC-SequenceStats</a> OPTIONAL,
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patch-type INTEGER {
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novel(0),
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fix(1),
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-- stopper
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other(255)
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} OPTIONAL,
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-- sequence-role: what role(s) does this sequence have in the assembly
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roles SET OF <a href="GC-SequenceRole.html">GC-SequenceRole</a> OPTIONAL
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}</pre>
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