The version v3.15.0 of the platform is now deployed.
The main novelty in this version is that we now use KEGG Orthology (KO) computed by KOfamScan to map genes to EC numbers and KEGG pathways instead of PRIAM results (see the documentation here). PRIAM results are no longer available in MicroScope (i.e. in the gene editor and in the Search by Keyword page).
Please also note that:
- KEGG maps are now displayed in a new tab (instead of a popup window)
- EC numbers associated to validated gene are no longer shown in red on the KEGG maps
- We have removed the Pathway Synteny page which was no longer practical with those modifications
- PRIAM is still used to predict pathways with the MicroCyc tool but we plan to change that soon.
Last but not least, sequence extraction didn’t work when the name of the replicon contained a space (or other special characters). This is now fixed.
Please report us any bugs you may meet.