ASAFind

ASAFind predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin, including plastid proteins and proteins targeted to the periplastidic compartment.

Key Features:

• Plastid protein prediction: Identifies nuclear-encoded plastid-localized proteins based on SignalP output and the conserved 'ASAFAP' motif and transit peptides.
• Periplastidic compartment prediction: Provides automatic prediction of PPC proteins, which was previously only possible through manual annotation.
• Multi-class targeting prediction: Distinguishes between plastid, PPC, and other intracellular locations in a single analysis.
• Compatibility with signal peptide predictors: Accepts output from SignalP (versions 3.0-5.0) and TargetP (versions 1.1 and 2.0).
• Graphical output: Generates visualization showing the contribution of each position in the sequence to the prediction score.
• Custom scoring matrices: Includes a script to calculate custom scoring matrices for simplified score cut-off mode predictions in other algal groups.

Scientific Applications:

• Plastid proteome identification: Genome-wide prediction of nuclear-encoded plastid-localized proteins in diatoms and algae with secondary plastids of the red lineage.
• PPC protein discovery: Identification of proteins targeted to the periplastidic compartment, such as the estimated 81 PPC proteins in Phaeodactylum tricornutum and 180 in Thalassiosira pseudonana.
• Comparative plastid biology: Adjustment of prediction methods to diverse algal groups through custom scoring matrices.
• Evaluation of signal peptide prediction tools: Benchmarking SignalP and TargetP versions for sensitivity and specificity in recognizing diatom signal peptides and cleavage sites.

Methodology:

ASAFind uses protein sequence data and external predictions of signal peptides by SignalP or TargetP, identifies conserved 'ASAFAP' motifs and transit peptides, and applies a scoring system to predict plastid and periplastidic compartment localization.