Abstract: Systems and methods for identifying sequence information from measurements made on single nucleic acid molecules are disclosed. The systems and methods can include binding portions of nucleic acid molecules with marker molecules, such as fluorescent molecules and/or intercalating molecules. The marker molecules provide a detectable signal that includes information about the underlying genomic information of the location on the nucleic acid molecule where a given marker molecule is bound. A profile of the detectable signal along a position of the nucleic acid is acquired for multiple different nucleic acid molecules. The PRIMR algorithm processes the data to provide a consensus profile from which a consensus underlying genomic information can be determined.

Abstract: Devices, systems, and methods for en masse patterning of nucleic acid molecule structures are disclosed. The devices can include microchannels and nanoslits. The microchannels and nanoslits can be connected by parking chambers. The systems and methods can utilize the geometry of the devices in coordination with a voltage application routine to park nucleic acid molecules in the parking chambers and subsequently inject the nucleic acid molecules into the nanoslits. The methods can be utilized to present nucleic acid molecules in a fashion suitable for genomic analysis. The methods can also be utilized to provide size selection of the nucleic acid molecules.

Abstract: Devices, systems, and methods for en masse patterning of nucleic acid molecule structures are disclosed. The devices can include microchannels and nanoslits. The microchannels and nanoslits can be connected by parking chambers. The systems and methods can utilize the geometry of the devices in coordination with a voltage application routine to park nucleic acid molecules in the parking chambers and subsequently inject the nucleic acid molecules into the nanoslits. The methods can be utilized to present nucleic acid molecules in a fashion suitable for genomic analysis. The methods can also be utilized to provide size selection of the nucleic acid molecules.

Abstract: Devices, systems, and methods for en masse patterning of nucleic acid molecule structures are disclosed. The devices can include microchannels and nanoslits. The microchannels and nanoslits can be connected by parking chambers. The systems and methods can utilize the geometry of the devices in coordination with a voltage application routine to park nucleic acid molecules in the parking chambers and subsequently inject the nucleic acid molecules into the nanoslits. The methods can be utilized to present nucleic acid molecules in a fashion suitable for genomic analysis. The methods can also be utilized to provide size selection of the nucleic acid molecules.

Abstract: Systems and methods for identifying sequence information from measurements made on single nucleic acid molecules are disclosed. The systems and methods can include binding portions of nucleic acid molecules with marker molecules, such as fluorescent molecules and/or intercalating molecules. The marker molecules provide a detectable signal that includes information about the underlying genomic information of the location on the nucleic acid molecule where a given marker molecule is bound. A profile of the detectable signal along a position of the nucleic acid is acquired for multiple different nucleic acid molecules. The PRIMR algorithm processes the data to provide a consensus profile from which a consensus underlying genomic information can be determined.

Abstract: Devices, systems, and methods for en masse patterning of nucleic acid molecule structures are disclosed. The devices can include microchannels and nanoslits. The microchannels and nanoslits can be connected by parking chambers. The systems and methods can utilize the geometry of the devices in coordination with a voltage application routine to park nucleic acid molecules in the parking chambers and subsequently inject the nucleic acid molecules into the nanoslits. The methods can be utilized to present nucleic acid molecules in a fashion suitable for genomic analysis. The methods can also be utilized to provide size selection of the nucleic acid molecules.

Abstract: There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Abstract: There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Abstract: There is provided a computer system for visualizing and editing single molecule fragments and one or more previously-produced single molecule assemblies or “contigs.” The present visualization and editing system allows a user to visualize large data sets resulting from single molecule map assembly operations, and to rapidly discern important features while errors and other discrepancies are conveniently resolved. The system includes one or more connectors connecting each to one or more databases capable of storing a diverse array of biomedical information, in addition to the single molecule data against which a user may validate the prior alignment and assembly. Embodiments described herein are thus useful in studies of macromolecules such as DNA, RNA, peptides and proteins. The visualization and editing system may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

Abstract: There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

Abstract: A computer database system for storing, processing, displaying, and analyzing single molecule data is capable of managing and processing variously formatted, different kinds of single molecule data and displaying subsets thereof upon instructions by a user. A component-based architecture is implemented where the processing and the displaying are separately performed. The data is dynamically loaded for processing as needed. Embodiments of computer database systems can be utilized in managing single molecule data, particularly image data derived from single molecule images. Such single molecule images may be generated by a variety of technologies, e.g., optical mapping, atomic force microscopy (AFM), scanning tunneling microscopy (STM), and flow cytometry. Systems may be deployed over a computer network. One or more additional databases may be included which are interconnected through a network.

Abstract: Laminar flow of a carrier liquid and polymeric molecules through micro-channels is used to straighten, align, separate, and/or sort the polymeric molecules. The polymeric molecules may be analyzed and/or manipulated in the carrier liquid or attached to a wall of the micro-channel for subsequent treatment and analysis. Micro-channels can be manufactured using an elastic molding material. One micro-channel embodiment provides fluid flow using a standard laboratory centrifuge.