[maker-devel] duplicate CDS in annotation

[Barry Moore]

Hi Sasha,

This gene model appears to be correctly formatted to me.  In GFF3 format the CDS features are allowed to span multiple lines and they share the same ID to indicate that it is all the same features.  See the GFF3 specification on the Sequence Ontology website (http://www.sequenceontology.org/resources/gff3.html), and in particular the description of the ID attribute specifies:

ID Indicates the ID of the feature. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature. 

So each of those CDS lines forms one part of the single CDS feature for this gene.

B
 
On Mar 11, 2013, at 3:46 AM, Sasha Mikheyev wrote:

> Dear Yandell lab,
> 
> I am re-annotating the harvester and genome using protein and RNA-seq data. However, I get many artifacts like the one below. It seems that there are several CDS records that should tie in to the same mRNA, but they are really hanging out separately, and produce several nucleotide sequences with the same name when extracted from the gff. I would appreciate any guidance about how to fix this!
> 
> Thank you,
> 
> Sasha
> 
> grep "pbar_scf7180000350377:hit:2506" Pbar.2.0.gff 
> pbar_scf7180000350377	protein2genome	protein_match	172004	172162	150	-	.	ID=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;score=150;
> pbar_scf7180000350377	protein2genome	match_part	172004	172162	150	-	.	ID=pbar_scf7180000350377:hsp:2798;Parent=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;Target=Hsal|HS9704 1 53 +;Gap=M159;
> pbar_scf7180000350377	maker	mRNA	538308	558769	.	+	.	ID=pbar_scf7180000350377:hit:2506;Parent=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29;Name=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29-mRNA-1;_AED=0.48;_eAED=0.39;_QI=0|0|0|0.5|1|1|6|0|395;score=0.01;
> pbar_scf7180000350377	maker	exon	538308	538334	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:305;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	exon	538748	538968	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:306;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	exon	539842	540242	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:307;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	exon	542624	542798	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:308;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	exon	555823	556025	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:309;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	exon	558609	558769	0.01	+	.	ID=pbar_scf7180000350377:hit:2506:exon:310;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	538308	538334	.	+	0	ID=pbar_scf7180000350377:hit:2506:cds:305;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	538748	538968	.	+	0	ID=pbar_scf7180000350377:hit:2506:cds:306;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	539842	540242	.	+	1	ID=pbar_scf7180000350377:hit:2506:cds:307;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	542624	542798	.	+	2	ID=pbar_scf7180000350377:hit:2506:cds:308;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	555823	556025	.	+	1	ID=pbar_scf7180000350377:hit:2506:cds:309;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377	maker	CDS	558609	558769	.	+	2	ID=pbar_scf7180000350377:hit:2506:cds:310;Parent=pbar_scf7180000350377:hit:2506;
> 
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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