Merging Information from different annotation Formate / files

[Carola Berger]

Hello guys,

I have a pretty basic question.

I have different annotation files from one organism (different file formats, like .embl, .gff, .gtf, .csv) and when I load them into Artemis they show a different amount of sometimes different Qualifier information for the same CDS. Is there a way to merge the information contained in those files into one file? And which file format should than be used?

I tried to use emboss featmerge but it only adds the different files together and I get multiple entries for the same CDS in the Panel list of Artemis.

Does anybody know anything?

Thanks a lot in advance!

[GenoMax]

If this is a known/model organism then look to see if a GTF or GFF file is available. That should include all annotation you need. If you post the name of the organism we can help you find the file, if one is available.

[Carola Berger]

yeah, it is a known model. It is Pseudomonas aeruginosa. And I do have multiple annotation files on it. I have a genbank file from NCBI and a gff file from NCBI and than I also have a gff file from the Pseudomonas Database and a embl and genbank file from them.

But the amount of information are quite different and I would like to have all the qualifieres in one file.

as an example here what the embl file and the gff file from NCBI give me on the gyrB gene:

embl:
/locus_tag="PA14_00050"
/db_xref="GeneID:4384102"
/name="gyrB"

gff:
/Name=gyrB
/ID=gene3
/locus_tag="PA14_RS00020"
/gene_biotype="protein_coding"
/gbkey="Gene"
/old_locus_tag="PA14_00050"
/gene="gyrB"

and for genbank it is also others. for some genes one file and for others another file has more info.

[GenoMax]

You would have to do the "merge" programmatically. Hopefully you have stable identifiers that can be used for cross-referencing the files. In the above example I only see the "gene" name as common entity, which may be a bit dicey to use as a "key". File from the Pseusomonas genome database should be the most complete I would think.

[Carola Berger]

well what is stable, is the location of the genes. Does that help?