Method and computer software product for predicting polyadenylation sites
Granted: September 4, 2003
Application Number:
20030167132
In one embodiment of the invention, computerized methods are provided for detecting polyadenylation sites and polyadenylation signals.
Methods for determining transcriptional activity
Granted: August 21, 2003
Application Number:
20030157529
In some embodiments of the invention, methods are provided to interrogate the transcriptional activity. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs in a cellular compartment.
System and method for programatic access to biological probe array data
Granted: August 21, 2003
Application Number:
20030157545
An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.
Apparatus and methods for constructing array plates
Granted: August 21, 2003
Application Number:
20030157700
In one embodiment, a method is provided for making an array plate for high throughput assays.
Monster capillary array electrophoresis scanner
Granted: August 14, 2003
Application Number:
20030150727
An improved rotary confocal fluorescence scanner capable of detecting analytes separated on over a 1,000 capillaries simultaneously. This system uses a confocal microscope objective and mirror assembly that rotates inside a vertical ring of capillaries to provide rapid and efficient excitation and detection of fluorescently labeled fragments separated within a cylindrical capillary array. Use of automated procedures to load and run all capillaries permits one to read more than 350,000…
Photocleavable protecting groups and methods for their use
Granted: July 31, 2003
Application Number:
20030144499
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 Ar—C(R1)(R2)—O—C(O)— wherein:
Polymorphism detection
Granted: July 17, 2003
Application Number:
20030134291
The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker,…
Identification of molecular sequence signatures and methods involving the same
Granted: July 10, 2003
Application Number:
20030129604
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,…
Methods and computer software products for designing nucleic acid arrays
Granted: July 10, 2003
Application Number:
20030130802
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 score.
Method and apparatus for providing a bioinformatics database
Granted: July 3, 2003
Application Number:
20030125882
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.
High throughput resequencing and variation detection using high density microarrays
Granted: July 3, 2003
Application Number:
20030124539
In one embodiment of the invention, methods and systems are provided for high thoughput genotyping. The system includes an automated sample preparation system, a sample tracking system, automated array processing and system for data analysis.
Method and computer software product for defining multiple probe selection regions
Granted: June 26, 2003
Application Number:
20030119007
In one embodiment of the invention, methods are provided for selecting probes upstream from alternative polyadenylation sites of a target sequence cluster.
Nucleotides and analogs having photoremovable protecting groups
Granted: June 26, 2003
Application Number:
20030119008
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. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
Arrays for detecting nucleic acids
Granted: June 26, 2003
Application Number:
20030119011
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.
Method and computer software product for genomic alignment and assessment of the transcriptome
Granted: June 26, 2003
Application Number:
20030120431
In one embodiment of the invention, computerized methods are provided for analyzing transcript sequence clusters by aligning the transcripts with genomic sequences to determine whether a cluster needs to be sub-clustered and whether clusters should be merged. In addition, in some embodiments, transcript sequences are trimmed according to their alignment with their corresponding genomic sequences. The modified clusters and trimmed sequences may be used for nucleic acid probe array design.
METHOD, SYSTEM AND COMPUTER SOFTWARE FOR ONLINE ORDERING OF CUSTOM PROBE ARRAYS
Granted: June 26, 2003
Application Number:
20030120432
A genomic portal system is described that receives user-selected identifiers of potential probes. The system determines verified probes corresponding to the identifiers and generates a custom probe array design. The system then displays the custom probe array design to the user via a graphical user interface and receives a user selection specifying acceptance, modification, or rejection of the design. The system provides the user with the accepted or modified custom probe array. The…
Apparatus and method for aligning microarray printing head
Granted: June 12, 2003
Application Number:
20030108868
An alignment apparatus and method are described for accurately and reliably depositing biological materials on a microscope slide or other substrate. A preferred implementation includes a first mounting assembly that enables rotation of deposit elements around a first axis perpendicular to the substrate surface using one or more bearing surfaces concentric with the first axis. A second mounting assembly enables rotation of the deposit elements around a second axis parallel to the…
Very large scale immobilized polymer synthesis
Granted: June 12, 2003
Application Number:
20030108899
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. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protecting groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
Method for detecting transcription templates
Granted: June 5, 2003
Application Number:
20030104367
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.
Human microarray
Granted: June 5, 2003
Application Number:
20030104410
Nucleic acid sequences are provided that are complementary, in one embodiment, to a wide variety of human genes. The sequences are provided in such a way as to make them available for a variety of analyses. As such, they are related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
