Feature transformation of phosphorylation sites for in silico prediction. The surrounding sequence of a phosphorylation site comprises 260 dimensions. Each dimension is defined by the position within the surrounding region and the amino acid type. The possible values in each dimension are 0 and 1. (a) Primary sequence (b) Extends set a by three dimensions, which include information about the predicted secondary structure of the phosphorylation site. (c) Extends set b by one dimension that contains the predicted accessibility. (d) Extends set a by three dimensions that reflect the conservation of the phosphosite in mammals and seven additional dimensions that describe the protein conservation in yeast, fly, zebrafish, chicken, cow, rat and mouse. (e) Combines set c and set d.
Gnad et al. Genome Biology 2007 8:R250 doi:10.1186/gb-2007-8-11-r250