Hi Torsten

Thanks for that. You are right that the sequences could be nucleotide or
protein. The behaviour therefore should probably be that it ignores any
non-base sequences and warns that it has done that. I will look at
implementing that change.


On 10/29/12 3:29 AM, "Torsten Seemann" <torsten.seem...@monash.edu> wrote:

> Tim,
> We commonly use multi-sequence GBK and GFF files. We know Artemis doesn't work
> with mult-GBK but it does work with GFF containing multiple source sequences
> (typically contigs) in the ##FASTA section. However, we are getting some GFF
> files that also have the translated protein sequences of each CDS feature in
> the ##FASTA section (much like CDS in GBK have /translation tags), like this:
> ##gff-version 3
> contig1 CDS ID=prot1
> contig2 CDS ID=prot2
>> >contig1
>> >contig2
>> >prot1
>> >prot2
> However, Artemis just treats the proteins as crazy DNA sequences and continues
> appending them to the list of source DNA sequences in the annotation.  I'm
> pretty sure this is a valid GFF file (as /translation may contain wierd AAs
> they aren't the original codon etc).
> So how to handle it in Artemis?
> Only display ##FASTA entries that have column1 IDs in the feature table?
> Should I RTFM ?
> Thanks for any help,

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