Genbank formatted output

[innovate-invent]

There are some barriers that will need to be overcome before Genbank format (or EMBL) can be supported for output.

Genbank supports a limited number of feature types, genomic islands not being one of them.
I emailed the NIH requesting advice on how to store unsupported features and they recommended using the misc_feature feature type. ex:

misc_feature    654..26955
                         /note="AbGRI1-5 genomic island"

This is not ideal as it places structured data in a free form text field.

If genomic islands can accurately be referred to as mobile elements then another feature was recommended:

mobile_element  3190..57412
                           /note="Integrative Element (IE)"
                           /mobile_element_type="other:Acinetobacter Genomic
                           Island 1 (AGI1)"

but this does not contain structured data identifying it as a genomic island.

My alternative proposal is:

mobile_element  3190..57412
                           /note="Integrative Element (IE)"
                           /mobile_element_type="other:genomic_island"
                           /standard_name="Acinetobacter Genomic
                           Island 1 (AGI1)"

This conforms to the Genbank standard here: http://www.insdc.org/files/feature_table.html
The mobile_element_type feature qualifier is defined as semi-structured data and genomic_island is the appropriate term from the Sequence Ontology. The Sequence Ontology also defines genomic_island as a descendant of mobile_genetic_element.

The other major barrier is that the stitcher currently generates invalid Genbank files. See brinkmanlab/galaxy-tools#5 and brinkmanlab/galaxy-tools#6 . The first linked issue could be resolved with brinkmanlab/galaxy-tools#8 but I doubt the second issue would be.

[innovate-invent]

Merging issue with #171