Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.

The invention is directed to methods and metric suitable for use in modulating the expression of a polypeptide encoded by a nucleic acid sequence. In certain aspects, the invention also relates to methods for introducing modifications in a polypeptide, for example through substitution of one or more nucleic acids in an untranslated sequence or in a coding sequence of a nucleic acid sequence encoding a polypeptide to increase the expression of the polypeptide.

There is provided a genome analysis device configured to analyze genome data including a large quantity of fragmented genome base sequences, and transmit output data concerning the genome data in response to an output request from a client device connected via a network, the genome analysis device including; a storage unit for storing data for visualization of multiple different layers, for the genome data; a request receiving unit for receiving an output request from the client device; and an output data generating unit for selecting data for visualization of a layer corresponding to the output request from the storage when the request receiving unit receives the output request, and generating output data based on the data for visualization of the selected layer.

The present invention relates to methods for the analysis of nucleic acids present in biological samples, and more specifically to normalize a high resolution melt curve to assist in the identification of one or more properties of the nucleic acids. The present invention provides methods and systems that incorporate a background identification algorithm according to invention principles using raw melt curve data to identify reactions that are unrelated actual DNA melt reactions. Furthermore, a web-based application for analyzing experimental data is provided. The raw experimental data obtained from a variety of instruments is processed and analyzed on a server and presented to a user through a user interface (UI).

Methods of evaluating or providing a clonal profile of a subject interval, e.g., a subgenomic interval, or an expressed subgenomic interval (or of a cell containing the same), in a subject, are disclosed.

Machine training and application of machine-trained classifier are used for image-based tumor phenotyping in a medical system. To create a training database with known phenotype information, synthetic medical images are created. A computational tumor model creates various examples of tumors in tissue. Using the computational tumor model allows one to create examples not available from actual patients, increasing the number and variance of examples used for machine-learning to predict tumor phenotype. A model of an imaging system generates synthetic images from the examples. The machine-trained classifier is applied to images from actual patients to predict tumor phenotype for that patient based on the knowledge learned from the synthetic images.

A system and method of selecting genes for a gene panel, includes retrieving gene-disease associations of genes associated with diseases at a given level in the disease hierarchy from a disease association database. The disease association database stores disease information, gene information, phenotype information, associations between diseases in the disease hierarchy, gene-disease associations and strength parameters related to the gene-disease associations. For each gene associated with the diseases at the given level, the strength parameters are weighted and combined to determine a rank score for the each gene. The genes are ranked based on the rank scores to provide ranked gene information. The ranked gene information is linked with diseases at the higher levels of the disease hierarchy based on hierarchical relationships. The ranked gene information for gene-disease associations can be used to select genes for a gene panel design.

Displaying an indication of ancestral data is disclosed. An indication that a genetic interval corresponds to a reference interval that has a likelihood of having one or more ancestral origins is received. One or more graphic display parameters are determined based at least in part on the indication. An indication of the one or more ancestral origins is visually displayed using the one or more graphic display parameters.

A sample processing apparatus (102) includes a plurality of processing stations (108) configured to process a sample that includes a DNA sample and an ILS substance carried by a sample carrier. One of the plurality of processing stations includes an electrophoresis processing station. The sample processing apparatus further includes an optical reader (110) that generates a plurality of DNA sample color group signals and an ILS signal based on a result of the electrophoresis processing station. One of the DNA sample color group signals includes at least the locus amelogenin X-peak. The sample processing apparatus further includes an ILS signal validator (112) that validates peaks of the ILS signal as true peaks of the ILS signal only if the amelogenin X-peak of the one of the DNA sample color group signals is found between two peaks of the ILS signal.

Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.