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Michael-Astbury avatar Michael-Astbury commented on July 28, 2024 1

Here's the head of the .gff:

##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM557713v1
#!genome-build-accession NCBI_Assembly:GCF_005577135.1
#!annotation-date 10/08/2023 12:45:54
#!annotation-source NCBI RefSeq 
##sequence-region NZ_CP040360.1 1 3081514
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2579791
NZ_CP040360.1	RefSeq	region	1	3081514	.	+	.	ID=NZ_CP040360.1:1..3081514;Dbxref=taxon:2579791;Is_circular=true;Name=ANONYMOUS;collection-date=2017-04-17;country=Singapore: near Pulau Ubin;culture-collection=PCC:11901;gbkey=Src;genome=chromosome;isolation-source=estuarine water [ENVO:01000301];lat-lon=1.421583 N 103.955722 E;mol_type=genomic DNA;old-name=Synechococcus sp. NTU 1704;strain=PCC 11901
NZ_CP040360.1	RefSeq	gene	1	378	.	+	.	ID=gene-FEK30_RS01170;Name=FEK30_RS01170;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01170;old_locus_tag=FEK30_01170
NZ_CP040360.1	GeneMarkS-2+	CDS	1	378	.	+	0	ID=cds-WP_138071278.1;Parent=gene-FEK30_RS01170;Dbxref=GenBank:WP_138071278.1;Name=WP_138071278.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FEK30_RS01170;product=hypothetical protein;protein_id=WP_138071278.1;transl_table=11
NZ_CP040360.1	RefSeq	gene	375	1010	.	-	.	ID=gene-FEK30_RS01175;Name=FEK30_RS01175;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01175;old_locus_tag=FEK30_01175
NZ_CP040360.1	GeneMarkS-2+	CDS	375	1010	.	-	0	ID=cds-WP_138071280.1;Parent=gene-FEK30_RS01175;Dbxref=GenBank:WP_138071280.1;Name=WP_138071280.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FEK30_RS01175;product=hypothetical protein;protein_id=WP_138071280.1;transl_table=11
NZ_CP040360.1	RefSeq	gene	1086	2045	.	-	.	ID=gene-FEK30_RS01180;Name=FEK30_RS01180;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01180;old_locus_tag=FEK30_01180
NZ_CP040360.1	Protein Homology	CDS	1086	2045	.	-	0	ID=cds-WP_138071282.1;Parent=gene-FEK30_RS01180;Dbxref=GenBank:WP_138071282.1;Name=WP_138071282.1;Ontology_term=GO:0016491,GO:0016651;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA,oxidoreductase activity%2C acting on NAD(P)H|0016651||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_013320252.1;locus_tag=FEK30_RS01180;product=Gfo/Idh/MocA family oxidoreductase;protein_id=WP_138071282.1;transl_table=11
NZ_CP040360.1	RefSeq	gene	2162	2455	.	+	.	ID=gene-FEK30_RS01185;Name=FEK30_RS01185;gbkey=Gene;gene_biotype=protein_coding;locus_tag=FEK30_RS01185;old_locus_tag=FEK30_01185
NZ_CP040360.1	Protein Homology	CDS	2162	2455	.	+	0	ID=cds-WP_138071284.1;Parent=gene-FEK30_RS01185;Dbxref=GenBank:WP_138071284.1;Name=WP_138071284.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017320150.1;locus_tag=FEK30_RS01185;product=ferredoxin;protein_id=WP_138071284.1;transl_table=11
NZ_CP040360.1	RefSeq	gene	2819	3112	.	+	.	ID=gene-FEK30_RS01190;Name=petF1;gbkey=Gene;gene=petF1;gene_biotype=protein_coding;locus_tag=FEK30_RS01190;old_locus_tag=FEK30_01190
NZ_CP040360.1	Protein Homology	CDS	2819	3112	.	+	0	ID=cds-WP_012307922.1;Parent=gene-FEK30_RS01190;Dbxref=GenBank:WP_012307922.1;Name=WP_012307922.1;gbkey=CDS;gene=petF1;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017320150.1;locus_tag=FEK30_RS01190;product=ferredoxin PetF1;protein_id=WP_012307922.1;transl_table=11

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m-jahn avatar m-jahn commented on July 28, 2024

I'm not aware of many more different types of annotation.
But you're right, in principle it should be possible to get features from various different sources. The default options are really just what I have encountered personally.

Can you paste the head of your annotation here? Would be useful to understand how this looks like.

I can imagine to simply add a list of different valid options/tags in the config.yml file. Then users can add their own when needed.

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