include more species on the species list

[amymc-uga]

On the FungAMR page, it was stated that there are 92 fungal species in the database whereas on the ChroQueTas it only included 52 species. I have checked my query species (Fusarium solani) is listed in the FungAMR database but I cant use it as a target species to run ChroQueTas. Is there a way for me to run ChroQueTas to search for the all 92 fungal species?

[nmquijada]

Dear @amymc-uga

Thank you for your comment, as we think it would be relevant for many other users. The FungAMR database contains all the information recovered from the massive literature screening, and includes the 92 species that we state.
However, many of the entries include features for resistance that are not resolved (yet) by ChroQueTas, including undefined fs, aneuploidy, overexpression, etc. Additionally, in order to be robust with the AMR phenotype, we decided to only include those AMR mutations for which a solid AMR evidence was reported for that mutation alone (this is, not in combination with other mutations).
On top of that, for some species and proteins we don't have a consistent reference protein to be used for the alignment and training of the model, but we are working hard to include as much as possible and to constantly update (this is an critical step, as a non-perfect reference might lead to spurious AMR profiling).

In the case of F. solani, we have two mutations reported for Myosin-5 with a high level of evidence: T218S and K376M.
However, we are still missing the consistent reference protein. If you have any hint, I would be happy to test the protein and include F. solani in the next release!

Additionally, I am considering adding a wiki tutorial to allow custom inclusion of proteins and mutations by the user. Although I hope that it does not lead to misleading interpretations...
I will clarify this inconsistency with the species numbers in the README of the next release (you can see v0.7.1 already available in a dedicated branch)

Looking forward reading your reply!
N