Abstract: A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.

Abstract: Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.

Abstract: In some embodiment of the invention, methods are provided for the synthesis of polymer arrays. In one embodiment, a reactive polymer and a photo acid generator is used for the photodirected polymer array synthesis.

Abstract: In one embodiment, fiber optic arrays or bundles are used as a light guide to transmit ultraviolet light to the substrate surface for photo-directed polymer synthesis. Digital Micromirror Array (DMA) is used as a switching device to reflect light onto the entry side of the fiber optic array.

Abstract: A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Abstract: Embodiments of the invention provide methods, computer software products and systems for detecting pixel stutter of a scanner. In one embodiment, a numeric count of stuttered pixels in both the x (row) and y (column) directions and a graphic display of the stuttered pixels overlaid on the image data are provided by the invention. The y-direction stutter count provides the estimate of pixel stutter from pure statistical data variations.

Abstract: Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.

Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence.

Abstract: A schema-isolated system is disclosed for developing, modifying, or maintaining client applications that accesses target databases. The system includes a middleware-table inserter that inserts middleware tables into the target database. The middleware tables include a set of compatibility data relating one or more client-application data requests with one or more corresponding target-database data capabilities. The middleware tables also include a data communication component. This component receives a client-application data request from the client application, and, based on at least a first datum of the set of compatibility data, provides to the client application the one or more target-database data capabilities corresponding to the client-application data request. The first compatibility datum relates the one or more client-application data requests with the one or more corresponding target-database data capabilities based, at least in part, on an application-usage-independent criterion.

Abstract: According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression or concentration information collected from large numbers of samples.

Abstract: Methods are provided for detecting the sense and antisense transcripts and for determining template strand of a genomic DNA. Exemplary methods include reverse transcribing transcripts without second strand synthesis. The resulting single stranded DNA is labeled and detected using nucleic acid probe arrays. In a particularly embodiment, actinomycin is used to inhibit the synthesis of second strand cDNA during reverse transcription.

Abstract: System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.

Abstract: Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.

Abstract: The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.