ELIXIR CZ Friday Coffee 2021 – ASAFind 2.0: Multi-class predictions of intracellular locations of proteins in organisms with complex plastids


Speaker: Ansgar Gruber from University of South Bohemia in České Budějovice and Biology Centre of the CAS

Plastids of diatoms and related algae with complex plastids of red algal origin, are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as cell biological processes take place in the PPC; however, genome wide predictions of the proteins targeted to this compartment were so far based on manual annotation work. Using published experimental protein localizations as reference data, we developed the first automatic prediction method for PPC proteins, which we included as a new feature in an updated version of the plastid protein predictor ASAFind. The new ASAFind version also accepts the output of the most recent versions of SignalP (5.0) and TargetP (2.0) as input data. Furthermore, we release a script to calculate custom scoring matrices, that can be used for predictions in a simplified score cut-off mode. This allows for adjustments of the method to other groups of algae.

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