  Cells of diatoms and related algae with complex plastids of red algal origin
are highly compartmentalized. These plastids are surrounded by four envelope
membranes, which also define the periplastidic compartment (PPC), the space
between the second and third membranes. The PPC corresponds to the cytosol of
the eukaryotic alga that was the ancestor of the complex plastid. Metabolic
reactions as well as cell biological processes take place in this compartment;
however, its exact function remains elusive. Automated predictions of protein
locations proved useful for genome wide explorations of metabolism in the case
of plastid proteins, but until now, no automated method for the prediction of
PPC proteins was available. Here, we present an updated version of the plastid
protein predictor ASAFind, which includes optional prediction of PPC proteins.
The new ASAFind version also accepts the output of the most recent versions of
SignalP (5.0) and TargetP (2.0) input data. Furthermore, we release a Python
script to calculate custom scoring matrices for adjustment of the ASAFind
method to other groups of algae, and included the option to run the predictions
with custom scoring matrices in a simplified score cut-off mode.
