#### README ####


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Download--Fasta
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Fasta DNA dumps
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FILE NAMES
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The files are consistently named following this pattern:
<species>.fna.gz

<species>: The abbreviated name of a species.
fna: All files in these directories represent FASTA database files
gz: All files are compacted with GNU Zip for storage efficiency.

EXAMPLES
	The genomic sequence of Populus trichocarpa:
	    PopTri.fna.gz



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Download--Protein
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Fasta Peptide dumps
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These files hold the protein translations of PPGR genes.

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FILE NAMES
------------
The files are consistently named following this pattern:
<species>.pep.gz

<species>: The abbreviated name of a species.
pep: All files in these directories represent FASTA database files
gz: All files are compacted with GNU Zip for storage efficiency.

EXAMPLES
	The protein sequence of Populus trichocarpa:
	    PopTri.pep.gz



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Download--Annotation
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GFF FLATFILE dumps
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Gene annotation is provided in GFF3 format.


The 'type' of gene features is:
 * "gene" for protein-coding genes
 * "ncRNA_gene" for RNA genes
 * "pseudogene" for pseudogenes
The 'type' of transcript features is:
 * "mRNA" for protein-coding transcripts
 * a specific type or RNA transcript such as "snoRNA" or "lnc_RNA"
 * "pseudogenic_transcript" for pseudogenes
All transcripts are linked to "exon" features.
Protein-coding transcripts are linked to "CDS" features.

Attributes for feature types:
(square brackets indicate data which is not available for all features)
 * gene types:
    * biotype: biotype, e.g. "gene", "pseudogene"
    * gene_id: gene stable ID
    * [Name]: Gene name
    * [description]: Gene description
 * transcript types:
    * Parent: Gene identifier, format "<gene_stable_id>"
    * biotype: biotype, e.g. "mRNA", "transcript"
    * transcript_id: transcript stable ID
 * exon
    * Parent: Transcript identifier, format "<transcript_stable_id>"
    * exon_id: exon stable ID 
 * CDS
    * Parent: Transcript identifier, format "<transcript_stable_id>"
    * CDS_id: CDS stable ID

-----------
FILE NAMES
------------
The files are consistently named following this pattern:
<species>.gff.gz

<species>: The abbreviated name of a species.
gff: All files in these directories are in GFF3 format
gz: All files are compacted with GNU Zip for storage efficiency.

EXAMPLES
	The annotation file of Populus trichocarpa:
	    PopTri.gff.gz