adding annotations from custom dna sequences (multifasta)

[rguerillot]

Would be great to have an option that allows to add annotations from custom dna sequences (eg. multifasta with sRNA). Like the --protein option, --dna option could be added. Ideally the user could set the blastn options for annotation (eg. e-value, %identity, %coverage).

Thanks for this great tool

Romain

[tseemann]

This is a good idea.

FYI, --proteins doesn't align the proteins however. It still requires Prodigal to find a gene. it is ony used to name the protein.

The --dna option would be different.