1. A method of determining one or more affinity parameters for predicting binding affinities of one or more nucleotide sequences, each defined by unique nucleotide sequence information, comprising: (a) obtaining one or more phenotypic measurements for said one or more nucleotide sequences; (b) linking said one or more phenotypic measurements to said one or more nucleotide sequences to obtain two or more linked pairs of said phenotypic measurements and said nucleotide sequences; (c) estimating a relationship between said one or more phenotypic measurements and said one or more nucleotide sequences using said two or more linked pairs; and (d) obtaining sequence specific affinity parameters from said estimated relationship.