Daniel Bunting (Nuffield student), Kentaro Yoshida and Diane Saunders at TSL.
We used the C. fraxinea KW1 predicted proteome (data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/annotations/Gene_predictions/TGAC_Chalara_fraxinea_ass_s1v1_ann_v1.1) as a basis to mine for candidate effectors.
- First, the predicted proteome of C. fraxinea KW1 was searched for potential secreted proteins using SignalP2 with parameters described in . Transmembrane domain containing proteins and proteins with mitochondrial signal peptides were removed using TMHMM  and TargetP , respectively.
- We then clustered all proteins using TribeMCL , following the methods described in . We identified clusters of proteins (known as tribes) that contained at least one secreted protein. These 593 tribes were then used for all further analysis.
- Next, we annotated the protein tribes for known effector features as described in .
- Finally, we assigned an e-value to each feature within a tribe using the method described in  in order to rank tribes based on their likelihood of containing effector proteins.
A spreadsheet that contains the above analysis is available at (data/ash_dieback/chalara_fraxinea/Kenninghall_wood_KW1/annotations/Effector_mining).
Figure 1. Pipeline used to mine for potential effector proteins in C. fraxinea KW1 isolate. Programs are indicated in red.
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