miRNA support in Tripal

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miRNA support in Tripal

Michael Dondrup-3
Hi,

we are planning to integrate de-novo miRNA predictions for our organism into LiceBase.
Therefore, I would like to ask if there is specific support for miRNA annotation existing or
planned in Tripal. In my opinion, miRNA are special for at least two reasons:

- we will do the predictions with miRDeep2 which generates bed files with coordinates for
precursors and mature miRNA, which we intend to upload both as features into Chado. Conversion
from BED to GFF should be possible by a script, using the mature miRNA as derived from the precursors.
Has anyone tried this before?

- annotation by Rfam/cmscan. While Blast could be used, we intend to also annotate using cmscan,
which doesn’t support Blast-like output afaik. We could put a single best hit into the Note field, but it would be handy,
to display all the cmsearch/cmscan hits  in the same way that Blast results are displayed under “Homology” on the feature page.
Is there any guidance in how to accomplish that?

Thank you
Michael

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