Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Abstract: The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.

Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.

Abstract: An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Abstract: Nucleic acid sequence determination is a method whereby peaks in data traces representing the detection of labeled nucleotides are classified as either noise or specific nucleotides. Embodiments are described herein that formulate this classification as a graph theory problem whereby graph edges encode peak characteristics. The graph can then be traversed to find the shortest path. Various embodiments formulate the graph in such a way as to minimize computational time. In various cases it is desirable that such classification allow for the possibility of mixed bases in the nucleotide sequence. Embodiments are described herein that address the classification of mixed-bases. Embodiments are also described that detail methods and systems for processing the data in order to make the classification step robust and reliable.

Abstract: A system and process for providing a transaction infrastructure for matching user demand for a commodity such as energy across multiple sources and levels of distribution. A transaction hub is provided that normalizes transaction information across a plurality of distribution points. Scheduling and billing of users is managed at the hub, allowing fine and dynamic load balancing across multiple sources and levels.