Methods and compositions for selecting tag nucleic acids and probe arrays
Granted: June 5, 2003
Application Number:
20030104436
Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.
Arrays for detecting nucleic acids
Granted: June 5, 2003
Application Number:
20030104411
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Cyclic and substituted immobilized molecular synthesis
Granted: May 29, 2003
Application Number:
20030099983
A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. In one particular embodiment, an array of rotated cyclic polymers is formed. In another embodiment, an array of polymers is formed based on a target polymer. The array includes systematically substituted versions of the target molecule. In another…
METHOD, SYSTEM AND COMPUTER SOFTWARE FOR VARIANT INFORMATION VIA A WEB PORTAL
Granted: May 29, 2003
Application Number:
20030100995
A genomic web portal is described that receives from a user over the Internet a selection of identifiers of probes for detecting biological molecules. The portal may also receive hybridization intensity values produced from biological probe array experiments. The portal determines alternative splice variants based on factors that may include the hybridization intensity values. The portal correlates alternative splice variants with annotation data and provides for the user a graphical…
Complexity management of genomic DNA
Granted: May 22, 2003
Application Number:
20030096235
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of…
Methods and computer software products for selecting nucleic acid probes
Granted: May 22, 2003
Application Number:
20030096986
Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, perfect match intensity, mismatch intensity and the slope of quantitative response of a probe are predicted. A unified quality score is calculated. Probes are selected based on the unified quality score.
Method of target enrichment and amplification
Granted: May 1, 2003
Application Number:
20030082543
The presently claimed invention provides methods and kits for amplifying a target sequence from within a nucleic acid population. The presently claimed invention provides selection probes which are complementary to at least a portion of said target sequence and mechanisms for adding a probe sequence to the 3′ end of a target sequence that is hybridized to a selection probe. The added 3′ probe sequence and a probe sequence added at the 5′ end of the target by adaptor…
Functionalized silicon compounds and methods for their synthesis and use
Granted: April 24, 2003
Application Number:
20030077650
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thio, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Methods, systems and software for gene expression data analysis
Granted: April 17, 2003
Application Number:
20030073125
Methods, computer software and systems are provided for biological data analysis. In one embodiment, a probe logarithmic intensity error resolver is provided to analyze gene expression data obtained using multiprobes.
Method and system for providing a polymorphism database
Granted: April 17, 2003
Application Number:
20030074363
Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The…
Apparatus for polymer synthesis
Granted: April 3, 2003
Application Number:
20030064391
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Capturing sequences adjacent to type-IIS restriction sites for genomic library mapping
Granted: March 27, 2003
Application Number:
20030059815
The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
Methods for polymorphism identification and profiling
Granted: March 20, 2003
Application Number:
20030054393
The invention provides methods of using probe arrays for polymorphism identification and profiling. Such methods entail constructing a first array of probes that span and are complementary to one or more known DNA sequences. This array is hybridized with nucleic acid samples from different individuals to identify a collection of polymorphisms. A second array is then constructed to determine a polymorphic profile of an individual at the collection of polymorphic sites. The polymorphic…
Conformationally-restricted peptide probe libraries
Granted: March 13, 2003
Application Number:
20030049674
Libraries of unimolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA. In a related aspect, the present invention provides libraries of conformationally restricted probes on a solid support. The probes are restricted in their movement and flexibility using…
Computer software system, method, and product for scanned image alignment
Granted: February 27, 2003
Application Number:
20030038812
A computer program analyzes an image including features that correspond to emissions detected from a biological probe array. The program aligns one or more grids, each having one or more grid cells, with all or portions of the image; selects one or more grid cells to be associated with features based on distributions of pixel intensity values within the grid cells; locates a shape, such as a circle, in each selected grid cell based on distributions of pixel intensity values within the…
Photocleavable protecting groups
Granted: February 27, 2003
Application Number:
20030040618
Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein: Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds…
Complexity Managment of genomic DNA
Granted: February 20, 2003
Application Number:
20030036069
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the…
Method, system, and computer software for the presentation and storage of analysis results
Granted: February 20, 2003
Application Number:
20030036087
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for…
Brassica polymorphisms
Granted: February 13, 2003
Application Number:
20030032025
The invention provides oligonucleotides and their complements that can be used as allele-specific probes or primers for sequencing, oligonucleotide probe hybridization, and allele-specific amplification. Such oligonucleotides can be used, for example, to facilitate genetic distinction between individual plants in plant populations.
Method and apparatus for imaging a sample on a device
Granted: January 23, 2003
Application Number:
20030017081
Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, can be detected by exposing selected regions of sample 1500 to radiation from a source 1100 and detecting the emission therefrom, and repeating the steps of exposition and detection until the sample is completely examined.
