Entering edit mode
5.2 years ago
sj93
▴
10
The IGB website says their program supports many different file formats, including gff. I have saved a genome from NCBI in several different file formats to my computer (using Ubuntu), but when I go to open the custom genome from IGB, it only recognizes the .fna file type, when I have genomes saved as .gbff and .gff in the same folder. It's like the program won't recognize these file types saved on my computer. Does anyone know why this might be happening? Thanks in advance.
Could you provide a sample of your gff fille ? Do you load the fasta separately or is it embedded in your gff ?
The fasta is not embedded, I tried it separately for comparison. I'm not sure what the best way to provide a link to my gff file would be, but the file is available on the top of the page at this location https://www.ncbi.nlm.nih.gov/genome/24088.
The GFF contains the annotation. It can sometimes contain the "genome sequence" using embedded FASTA that Juke-34 refers to, but more often the genome sequence is in a FASTA file (extension .fa, .fasta, or .fna sometimes from NCBI). You can download the FASTA from NCBI too and probably will open that first and then the annotation as GFF
Thank you very much! :)
This gff file is completely stupid, never seen that before. It doesn't contain anything interesting, no structural annotation (position of feature like gene, trna, pseudogene, etc). It looks like description of sequences of an assembly. It describes the size of 80 000 sequences. So it's a gff of an assembly... I'm wondering how useful that could be ???
So according to this gff file there is nothing to display, so it's normal you don't see anything in IGB.
This is a mitochondrial genome (not a full genome) AFAI see.
She/he said at the top of the page...
I don’t think she/he talks about the mitochondrial genome.