Array design facilitated by consideration of hybridization kinetics

摘要

Methods, systems and computer readable media for selecting probes for design of a chemical array. A first set of candidate probes is provided for hybridization with a sample at a first hybridization stringency and a second set of candidate probes identical to the first set is provided for hybridization with the sample at a second hybridization stringency. After hybridizing the first set with the sample at the first hybridization stringency and the second set with the sample at the second hybridization stringency higher than the first hybridization stringency, the relative change in signal extracted from a probe in the first set relative to the same probe in the second set is calculated, and this calculation is carried out for each of a plurality of (up to and including all) other probes in the first set and same probes in the second set, respectively. At least the probe having the highest calculated relative change in signal between the first and second hybridization stringencies is eliminated as a candidate for use in the array design. Methods, systems and computer readable media for identifying relative degrees of non-specific binding of probes hybridized with a sample. A first set of probes is provided for hybridization with a sample at a first hybridization stringency and a second set of probes identical to the first set is provided for hybridization with the sample at a second hybridization stringency. After hybridizing the first set with the sample at a first hybridization stringency and hybridizing the second set with the sample at a second hybridization stringency higher than the first hybridization stringency, the relative change in signal extracted from a probe in the first set relative to the same probe in the second set is calculated, and this calculation is repeated for each of a plurality (up to, and including all) of other probes in the first set and same probes in the second set, respectively. The probes are then ranked by degree of non-specific binding, wherein the probe having the highest calculated relative change in signal between the first and second hybridization stringencies is ranked highest.