prodigal prediction frame

[Intikhab]

Dear Prodigal Developers,

I regularly use Prodigal in my microbial genomes analysis and it is very impressive gene predictor.

Can I know how can I get the correct gene prediction frame information in Prodigal's GFF output?

At present I see it prints frames as 0 all the time.

Many Thanks,

Intikhab

[dhyatt1]

My understanding of the frame field in GFF is that it is supposed to report the reading frame of exons relative to a gene, which only changes in the case of splice sites interrupting codons in genes with introns.

So this field is always '0' for microbial genes.  The one exception might be if Prodigal reported partial genes as (1..100), but it does not; it reports them as (<2..100), so you can always deduce the frame from

the coordinates.

regards,

doug