α score distribution. Panel a: Distribution of α scores for missing genes, missing gene groups, and absent annotations. Panel b: Distribution of alpha scores for missing genes from groups that do and do not have a representative alignment to nr-aa. Density refers to kernel density [41,42]. Kernel density graphs were generated using the R sm package [42,43], where the bandwidth (smoothing parameter) is calculated as the mean of the normal optimal values for the different groups. Kernel density plots can be thought of as smooth histograms using a Gaussian function centered at each observation, instead of a box. This explains why the left and right tails extend beyond the defined bounds of the α function (0 and 100).
Warren et al. BMC Bioinformatics 2010 11:131 doi:10.1186/1471-2105-11-131