Abstract: Various aspects of the invention include a solid support having a first region with a first nucleic acid, and second, third, fourth and fifth regions having, respectively, second, third, fourth, and fifth nucleic acids each having a length that is shorter than the length of the first nucleic acid. Certain aspects of the invention further include embodiments where the second, third, fourth, and fifth nucleic acids are substantially identical, and no two of the second, third, fourth, and fifth nucleic acids ends with identical terminal nucleotides. Some aspects of the invention further include methods of using the solid support, and kits that include the same.

Abstract: In an embodiment, a method is included for generating a negative control probe sequence for an array including selecting biological probe sequences from the array randomly, generating a plurality of candidate probe sequences by randomly permuting the selected biological probe sequence, and screening the candidate probe sequences for sequence similarity to biologically occurring sequences. An embodiment also includes a computer-readable medium having computer-executable instructions for performing a method for generating a negative control probe sequences. Embodiments can also include an apparatus for generating a negative control sequence for an array, as well as negative control probes, sets of negative control probes and arrays comprising at least one negative control probe.

Abstract: The invention relates to methods and systems for generating negative controls for arrays. In an embodiment, the invention includes a method for generating a negative control probe sequence for an array including randomly generating a plurality of candidate negative control probes, screening the candidate negative control probes for sequence similarity to biologically occurring sequences, and screening the candidate negative control probes for one or more of base composition properties, primary structural features, secondary structural features, or thermodynamic characteristics. In an embodiment, the invention includes an apparatus for generating a negative control sequence for an array.

Abstract: A method and apparatus of interrogating an addressable array unit, which includes a substrate, a light reflecting layer on a front side of the substrate, and a plurality of features on a front side of the array. The method may include, for each of multiple features, illuminating the feature simultaneously with reflected and non-reflected interrogating light. A light emitted from respective features is detected. Either or both, constructive interference of interrogating light at the features, or constructive interference of light emitted from the features, can be obtained to allow lowering of light power from the source, enhanced signal, or reduced noise, or combinations of the foregoing. High depth discrimination may also be obtained without the need for a confocal detection system with conventional pinhole.

Abstract: Methods for evaluating surface-bound polynucleotides, e.g., candidate aCGH probe nucleic acids, are provided. Specifically, the methods involve contacting an array of surface-bound polynucleotides with a validation nucleic acid composition and assessing binding of the surface-bound polynucleotides. The methods may be used to screen for surface bound polynucleotides that have desirable binding characteristics, e.g., suitability for use in array-based comparative genomic hybridization assays.

Abstract: Methods and systems for selecting oligonucleotide probes for use in microarray applications are provided herein. The described methods use a combination of measured probe performance and predicted probe performance to select probes. Nucleic acid arrays containing probes selected by the described methods are described. Also included are algorithms for performing the subject methods recorded on computer-readable media and computational systems for analysis.

Abstract: Methods for correcting systematic errors in the measured position of deposited features of a nucleic acid array on a substrate. Systematic errors are modeled by an algorithmic model based on measuring the positions (and possibly other properties) of a subset of the features, and a model is constructed for predicting deviations in feature position from an ideal grid. Deviations arising in the deposition process, the scanning process, or both may be corrected.

Abstract: The present invention provides various embodiments that are directed to methods and systems for determining a feature-coordinate grid of a microarray image so that individual features can be located and isolated for statistical analysis. The method receives microarray-image data and determines centroid coordinates for each feature of the microarray image. The methods and systems of the present invention determines uses the centroid coordinates to determine horizontal grid lines and vertical grid lines that are superimposed on the microarray image so that intersections of the grid lines coincide with features of the microarray image. The horizontal grid lines and vertical grid lines provide grid lines of the feature-coordinate grid.

Abstract: A method of reading an assay includes illuminating a substrate. The substrate includes a sensitive region. The method also includes detecting whether the substrate was exposed to an analyte of interest. The detecting includes using low resolution detection and a priori data about the sensitive region to determine whether a characteristic of a first portion of the illumination returned from the sensitive region differs from a characteristic of a second portion of the illumination returned from the substrate outside the sensitive region.

Abstract: The present invention provides a method of performing an array hybridization analysis of a sample, including performing a restriction digest reaction on the sample, hybridizing the digested sample to the array, and interrogating the array. The array includes probe sets that provide for a determination of the extent of the restriction digest performed on the sample. Arrays including the probe sets are also described.

Abstract: Nucleic acid arrays that include a set of hybridization parameter probe features are provided. Also provided are methods of using the subject arrays in hybridization assays. In certain aspects, signals detected from the hybridization parameter probe features may be employed to determine a hybridization parameter of the assay. The subject arrays and methods find use in a variety of different applications. Also provided are computer programming, devices that include the same and kits that find use in practicing the subject methods.

Abstract: Methods and systems for analyzing comparative genomic hybridization data. The methods comprise measuring comparative genomic hybridization data, and applying a shaped response function to the comparative genomic hybridization data, wherein the shaped response function has a central maximum. The comparative genomic hybridization data may be obtained from a comparative genomic hybridization array. The shaped response function in many embodiments is symmetrical in shape tapers to zero on each side of said central maximum.

Abstract: The present invention relates to methods for detecting, quantitating, or standardizing binding to a nucleic acid array, standard polynucleotides that can be used in such methods, compositions including the standard polynucleotides, and methods of making the standard polynucleotides. An aspect of the present invention relates to a complete exon transcript of a gene. The gene can be a gene expressed as multiple transcripts but encoding only transcripts lacking at least a portion of at least one exon. A complete exon transcript includes all of the known bases of every known exon for such a gene. An aspect of the present invention relates to a method of detecting binding to a nucleic acid array. The method can include contacting the nucleic acid array with a standard polynucleotide for a gene. The standard polynucleotide for a gene includes all of the known bases of every known exon for that gene. In an embodiment, the standard polynucleotide includes a complete exon transcript of the gene.

Abstract: Methods, systems and computer readable media for identifying dye-normalization probes. Intensity signals read from probes on a set of existing multi-channel microarrays are provided. The intensity signals are combined from each channel for each probe to generate a combined signal intensity value for each probe on each array. For each probe, the combined signal intensity values are combined across all arrays to provide an ordered sequence of probes from a lowest overall signal to a highest overall signal. The probes are then ranked according to the results of combining the combined signal intensity values, and binned into a plurality of bins. With regard to each probe, a metric representative of the multi-array distance of the signal intensities of the probe from a neutral expression value across all arrays is calculated and the probes are ranked within each bin based on the calculated metrics.

Abstract: One embodiment of the present invention provides a method and system for selecting a subset of normalization features, or biomolecule probes, from multiple data sets generated from a single microarray and from multiple data sets generated from multiple microarrays. In this embodiment, the signal intensities corresponding to common features within the data sets are viewed as generating a distribution of features within an n-dimensional signal-intensity distribution. One or more order-preserving sequences of features within the n-dimensional signal-intensity distribution are determined using an efficient, two-pass-per-dimension method. Normalizing features then selected from the one or more order-preserving sequences. Normalizing data points from generalized data sets may be obtained by using embodiments of the present invention.

Abstract: Systems and methods for optimizing polymer analysis are provided. One such system includes a polymer analysis system having a polymer control system. The polymer analysis system is operative to: apply a set of conditions to a sample being analyzed by the polymer array, the set of conditions correspond to at least one characteristic of the polymer array; analyze the at least one characteristic using the polymer control system; and generate polymer array data.

Abstract: A method and system for detecting block and zone misalignment of feature positions within a microarray-data set and for correcting feature positions for block or zone misalignment. In one embodiment of the present invention, displacement vectors representing the vector differences between observed positions of features and expected positions for the features of a microarray are calculated, based on an initially determined coordinate system. Features within a microarray data set are then partitioned with respect to the calculated vector displacements, so that features misaligned by a common rotation or translation are partitioned into a separate partition. A correction for each common misalignment can then be calculated and applied to the features of each partition.

Abstract: A technique for analyzing target chemicals is provided. The apparatus of the technique contains an array of two or more light sources. Each of the array elements includes a light source. The light source has an emitting surface from which light can be emitted. Two or more binder chemical moieties are associated with the light sources at the emitting surfaces. These binder chemical moieties can bind target chemicals such that different target chemicals can be bound to the array. Light emitted by the light sources impinges on target chemicals bound to the light sources and will cause light interaction (e.g., fluorescence) with the target chemicals to result in a light pattern or patterns to indicate the presence or quantity of the target chemicals. The array is formed by a tiling technique involving the arrangement of tiles of array elements in a desired pattern.

Abstract: An optical scanning apparatus for scanning an array of sample regions carried on the surface of a substrate is disclosed. The apparatus includes a beam generator for generating a light beam effective to produce detectable light from such sample regions, and scanning optics for scanning the beam in one direction corresponding to a linear array of such sample regions. Light emitted from the linear array is imaged through an imaging system whose optical axis is angularly offset from the optical axis of the illumination beam, onto a photodetector. The optical configuration achieves high performance with relatively simple optics.

Abstract: Disclosed herein is an improved passive ring laser gyroscope with two systems: common mode and differential mode error systems. The common mode error system modulates counter propagating coherent radiation. The modulated light from a common source is split at a beam splitter before the reasonator cavity and then optically recombined at the same beam splitter for further propagation to an electronic detecting and demodulation servo system. The resulting electronic error signal is used to adjust the ring resonator and the laser so that the frequency output of the coherent radiation of the laser is substantially equal to the resonance frequency of the ring resonator. The differential mode error system optically substracts counter propagating radiation signals emanating from the resonator cavity to form a differential error signal that is detectable by an electronic detector for further processing by demodulation.