Gene birth contributes to structural disorder encoded by overlapping genes

S. Willis; J. Masel

We used IUPred [12] to calculate ISD values for each sequence. Following [52] , before running IUPred, we excised all cysteines from each amino acid sequence, because of the uncertainty about their disulphide bond status and hence entropy [49] . Whether cysteine forms a disulphide bond depends on whether it is in an oxidizing or reducing environment. IUPred implicitly, through the selection of its training data set, assumes most cysteines are in disulphide bonds, which may or may not be accurate for our set of viral proteins. Because cysteines have large effects on ISD (in either direction) depending on disulphide status and hence introduce large inaccuracies, cysteines were dropped from consideration altogether.