Abstract: A system for measuring and analyzing an image of a gel electrophoresis, includes measuring apparatus and a processor. The measuring apparatus includes a frame mountable in a fixed location relative to the image, including a bar extending along a first axis, a carriage coupled to the bar and slidable along the first axis, an alignment device extending transversely from the carriage along a second axis for aligning selected components of the image, and a distance sensor operatively coupled to the carriage for sensing the distance travelling by the carriage and generating distance signals. The processor is operatively coupled to the measuring apparatus and processes the distance signals and generates maps based thereon. The subject system is well suited for constructing restriction enzyme maps for an image of bands created by subjecting DNA to gel electrophoresis.

Abstract: This invention relates to a system and methods for the straightening an electrophoresis gel image in the vertical and horizontal directions, and for analyzing a straightened gel image. The system includes an input unit for receiving raw data from the electrophoresis gel, a straightening unit for providing a straightened gel image, an output unit for portraying the raw data from the electrophoresis gel and the straightened gel image, and a an analyzing unit for analyzing the data portrayed in the straightened gel image. The system features a dye boost feature for boosting the intensity of bands, filtering means for modifying the gel image, and a genotype editing feature for editing the results of an automatic gel analysis. The system allows for manual and automatic analysis of the straightened gel image according to a specified set of analysis parameters providing a range of analysis stringency levels.

Abstract: In a DNA base sequencing, a consensus sequence is obtained by linking a plurality of DNA fragments obtained by a DNA sequencer, and a base sequence to be edited is determined in the consensus sequence. Then, a trace corresponding to the determined base sequence to be edited is identified among traces obtained by the DNA sequencer. The identified trace is displayed in correspondence with the base sequence to be edited. At this time, the base sequence to be edited is displayed so that an interval between bases becomes even.

Abstract: A suite of tests and parameter monitoring methods for at least five major subsystems that are found in most automated image processing systems, as well as calibration routines for three major system functions. The five areas of subsystem verification include processing quality, illumination quality, image collection quality, autofocus quality, and position quality. An automated biological specimen analysis system uses self measures of system parameters to provide a system status. The system status is reported to the user.

Abstract: Normalization of experimental fragment patterns for nucleic acid polymers having putatively known sequences starts with obtaining at least one raw fragment pattern for the experimental sample. The raw fragment pattern represents the positions of a selected nucleic acid base within the polymer as a function of migration time or distance. This raw fragment pattern is conditioned using conventional baseline correction and noise reduction technique to yield a clean fragment pattern. The clean fragment pattern is then evaluated to determine one or more "normalization coefficients.

Abstract: The invention is an optical feature extraction apparatus which uses video display, spatial light modulation, and detection components in conjunction with microlenslet replicating optics, to expedite the recognition of DNA sequences based on their symmetry properties and, specifically, to classify short (6 bases in length) sequences of DNA as palindrome or nonpalindrome. The DNA sequences are symbolically encoded using a novel method. Multichannel operation is achieved through the replication of input scenery, making possible a higher throughput rate than for single channel systems.

Abstract: The present invention provides methods of determining relative copy number of target nucleic acids and precise mapping of chromosomal abnormalities associated with disease. The methods of the invention use target nucleic acids immobilized on a solid surface, to which a sample comprising two sets of differentially labeled nucleic acids are hybridized. The hybridization of the labeled nucleic acids to the solid surface is then detected using standard techniques.

Abstract: A method and apparatus for detecting rare cells in a biological sample is disclosed. A color image of the sample is generated and the color image is decomposed into its color components. A first mask is then generated based upon a first color characteristic of the rare cells. At least one color component of the color image is filtered using the mask to produce at least a first composite image which contains features having the first color characteristic. At least a second mask is then generated based upon other color characteristics of the rare cells and at least the first composite image is filtered using at least the second mask to create at least a second composite image. The color and/or shape of features in the at least second composite image are analyzed and a list of locations of probable rare cells is generated from the color and/or shape analysis.

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: A method and apparatus for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence.

Abstract: A method and system for searching for a given sequence in a data base having a multitude of reference sequences stored or identified therein. In accordance with this method, a light beam is modulated with patterns representing the reference sequences, and with a pattern representing the given sequence, and a correlation signal is generated representing the correlation of the reference and given sequences.Optical diffraction patterns may be used to represent the given and reference sequences. In one embodiment, a multitude of first diffraction patterns, each one representing the given sequence, are formed in an optical medium, and a light beam is modulated with each of those multitude of diffraction patterns to form a multi-channel signal beam. Each channel of that beam is then modulated with a respective one second diffraction pattern representing one of the reference sequences to form a multi-channel correlation beam.

Abstract: A method for determining the location and density of bands of biopolymers which are formed by developing and resolving a mixture of biopolymers on a supporting medium in one direction to form a lane of plural bands. The method includes the steps of inputting an image of the lane to a computer in the form of digital data comprising information of location and density, displaying the image, and setting a belt area along the lane which encompasses the aimed bands of the biopolymer. The belt area is then scanned a plurality of times in parallel directions crossing the lane with sufficiently small spacing so as to scan every band present within the belt area, in order to detect relationships of location and density on the digital data in the direction of the lane within the belt area. One dimensional data is then prepared to enable a determination of the location and density of the aimed bands.

Abstract: A system for identification of DNA bases in a nucleotide sequence includes a microprocessor and a set of executable instructions and is configured to accept a set of input data corresponding to a DNA sequence image from an autoradiograph. In part by interpolating a distribution of density peaks derived from the set of input data, the system is configured to generate a set of output data substantially identifying or presenting the bases in the DNA sequence in a linear fashion, corresponding to the linear order of nucleotides comprising the DNA sequence. The system thereby enables identification of substantially more bases than could be read by the human eye. Enhanced electrophoresis equipment and consumables may also be applied to generate a more predictable and linear set of input data and, in turn, to generate a set of output data identifying an even greater number of DNA bases in the sequence under analysis.

Abstract: Cell samples, stained with a fluorescent dye, taken up by DNA in the individual cells, are scanned with a cytometer, which measures the integrated value of fluorescent light/cell. The integrated values of all of the cells are compiled to create an histogram of cell counts versus integrated fluorescent light, representing a cell population of (a) cells having a complement of DNA, but not in the process of division (G.sub.0 phase), (b) cells having two full compliments of DNA, but which have not actually divided into two cells (G.sub.2 phase) and (c) cells which are in the process of replicating their DNA (S, separation phase). The percentages of cells in each of the phases, represented in the histogram as separated peaks of sizes proportional to the G.sub.0 and G.sub.2 populations, and separation S phase population, aids in the prognosis of a patient's cancer development. More serious malignancy is indicated by increased S and G.sub.2 phase populations. Errors, e.g.

Abstract: A genetic motif extracting apparatus is adapted to extract a motif from genetic sequence information, where the motif has a regularity in a distinctive feature that specifies a genetic function. The genetic motif extracting apparatus includes a weight calculation unit for calculating a weight of each genetic sequence from a length of at least one branch of an evolution tree structure that is related to a plurality of genetic sequences, a score calculation unit for calculating a score that indicates a degree of similarity of sequence elements of the genetic sequences appearing at a site for each site of the genetic sequences using the weight calculated by the weight calculation unit, and a feature information extraction unit for extracting a part of the genetic sequence having the regularity in the distinctive feature as the motif based on the score calculated by the score calculation unit.

Abstract: The present invention pertains to a process which can be fully automated for accurately determining the alleles of STR genetic markers. More specifically, the present invention is related to performing PCR amplification on a location of DNA, labelling the PCR products, converting the labels into a signal, removing a reproducible PCR stutter pattern from the signal by means of a computational device, and then determining the genotype of the location of the DNA. The invention also pertains to genetics applications and systems which can effectively use this genotyping information.

Abstract: An operator independent image cytometer having a method for image segmentation. Image segmentation comprises the steps of filtering a digital image of a cellular specimen and thresholding the resultant image. In addition, the thresholding may include the sorting of features extracted from the filtered image. The present invention also includes a method for cytometer autofocus that combines the benefits of sharpening and contrast metrics. The present invention further includes an arc lamp stabilization and intensity control system. The image cytometer has broad applications in determining DNA content and other cellular measurements on as many as 10.sup.5 individual cells, including specimens of living cells. Image segmentation applications include PAP smear analysis and particle recognition.

Abstract: A method and apparatus are provided for selecting and analyzing a subpopulation of cells or cell objects for a certain parameter such as DNA using image analysis means. The cells are first stained with an alkaline phosphatase technique including a monoclonal antibody specific to a protein in at least one of the cell's cytoplasm or on a cell membrane, thereby marking any cells including the protein as to type. A second staining of the DNA in the nucleus is accomplished by a Feulgen technique that destroys the cell cytoplasm. After the staining and marking, the cells may then be gated using the image analysis means on the visual parameter such as colored DNA or colored antigen into a subpopulation that is to be measured. The selected cells may then be examined by digital image processing and measured for a parameter such as a true actual measurement of DNA in picograms. A quantitation of the measured parameter may be generated and provided.

Abstract: The present invention pertains to a process which can be fully automated for accurately determining the alleles of STR genetic markers. More specifically, the present invention is related to performing PCR amplification on locations of DNA, labelling the PCR products, converting the labels into a signal, removing a reproducible PCR stutter pattern from the signal by means of a computational device, and then determining the genotype of the location of the DNA. An amplification can include multiple locations from the DNA of one or more individuals. The invention also pertains to genetics applications and systems which can effectively use this genotyping information.

Abstract: A method and apparatus for the processing of DNA sequence image data in real time is implemented using a series of linked neural network processors. As raw image data is received from a sequencing machine, it is buffered and then separately transformed in real time in the processors to enhance the signals indicative of the unknown DNA sequence. A fourth processor receives the transformed data and determines and reports the sequence indicating events.