Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.

Abstract: Exemplary embodiments provide methods and systems for string graph assembly of polyploid genomes. Aspects of the exemplary embodiment include receiving a string graph generated from sequence reads of at least 0.5 kb in length; identifying unitigs in the string graph and generating a unitig graph; and identifying string bundles in the unitig graph by: determining a primary contig from each of the string bundles; and determining associated contigs that contain structural variations compared to the primary contig.

Abstract: Exemplary embodiments provide methods and systems for string graph assembly of polyploid genomes. Aspects of the exemplary embodiment include receiving a string graph generated from sequence reads of at least 0.5 kb in length; identifying unitigs in the string graph and generating a unitig graph; identifying string bundles in the unitig graph; determining a primary contig from each of the string bundles; and determining associated contigs that contain structural variations compared to the primary contig.

Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.

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: Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.

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: A system for performing quality control for nucleic acid sample sequencing is disclosed. The system has a set of solid supports, each support having attached thereto a plurality of nucleic acid sequences. The set has plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived. A method of preparing a quality control for performing nucleic acid sample sequencing and a method of validating a nucleic acid sequencing instrument are also disclosed.

Abstract: An integrated article of footwear including a waterproofing membrane direct attached to an upper of the footwear. An outsole is further secured to the membrane and/or the upper. In one embodiment, the membrane includes a visible aesthetic bead in the footwear forefoot region, but not the heel region. The membrane may be of greater thickness in the forefoot region to provide added rigidity. A heel cradle is positioned in the footwear heel region between the upper and the outsole. The footwear provides the durability of a direct attach construction in the forefoot and the comfort and cushion of an athletic construction in the heel of the shoe. A method for constructing the footwear includes direct attaching the membrane to an upper of the shoe. Optionally, a heel cradle is disposed in the heel region of the shoe, and the outsole is secured to the heel cradle and/or upper there.

Abstract: An integrated article of footwear including a waterproofing membrane direct attached to an upper of the footwear. An outsole is further secured to the membrane and/or the upper. In one embodiment, the membrane includes a visible aesthetic bead in the footwear forefoot region, but not the heel region. The membrane may be of greater thickness in the forefoot region to provide added rigidity. A heel cradle is positioned in the footwear heel region between the upper and the outsole. The footwear provides the durability of a direct attach construction in the forefoot and the comfort and cushion of an athletic construction in the heel of the shoe. A method for constructing the footwear includes direct attaching the membrane to an upper of the shoe. Optionally, a heel cradle is disposed in the heel region of the shoe, and the outsole is secured to the heel cradle and/or upper there.

Abstract: A sealing structure capable of withstanding water pressure, which has a zipper on two sides of a flexible member at an opening of a container, one margin of the opening is a vertical extension of a buffer plate. Fitted to one end of the buffer plate is a pillar-shaped inside fastener unit. Another margin of the opening is a vertical extension of a buffer plate, fitted to one end of the buffer plate is a C-shaped outside fastener unit. By closing the opening with the zipper, wrapping of the inside fastener unit by the outside fastener unit, and an additional C-shaped exterior wrapping strip wrapping the outside fastener unit, so the inside and outside fastener units are completely and firmly combined to completely seal the opening of a flexible container, and water is kept from seeping in, thereby achieving its sealing purposes to resist water and withstand water pressure.

Abstract: An integrated article of footwear including a waterproofing membrane direct attached to an upper of the footwear. An outsole is further secured to the membrane and/or the upper. In one embodiment, the membrane includes a visible aesthetic bead in the footwear forefoot region, but not the heel region. The membrane may be of greater thickness in the forefoot region to provide added rigidity. A heel cradle is positioned in the footwear heel region between the upper and the outsole. The footwear provides the durability of a direct attach construction in the forefoot and the comfort and cushion of an athletic construction in the heel of the shoe. A method for constructing the footwear includes direct attaching the membrane to an upper of the shoe. Optionally, a heel cradle is disposed in the heel region of the shoe, and the outsole is secured to the heel cradle and/or upper there.

Abstract: A compass cutter has a main body fastened with an extension rod which is connected with a slidable seat slidable along the extension rod. The main body is further provided with a locating block, a protective cover, a blade, a fixation block, and an insertion pin. The slidable seat is provided with a locating block, a connection rod, a locating pin, and a shield. The compass cutter can be expanded, through the movement of the extension rod. The locating pin and the blade are covered by the shield to protect the user of the compass cutter.

Abstract: A modular container is formed of a casing, a seat ring, a rotary cover, and a base. The casing is provided with a plurality of retaining holes and retaining projections. The seat ring is located in the top of a cylindrical object which is formed by the casing. The base if disposed at the bottom of the cylindrical object. The rotary cover is provided with a plurality of retaining protrusions. The seat ring is provided with a plurality of locating slots. The rotary cover is located by the seat ring such that the retaining protrusions of the rotary cover are located in the locating slots of the seat ring.

Abstract: A compass cutter comprises a main body fastened with an extension rod which is connected with a slidable seat slidable along the extension rod. The main body is further provided with a locating block, a protective cover, a blade, a fixation block, and an insertion pin. The slidable seat is provided with a locating block, a connection rod, a locating pin, and a shield. The compass cutter can be expanded, thanks to the extension rod. The locating pin and the blade are shield by the shield to protect the user of the compass cutter.

Abstract: A modular container is formed of a casing, a seat ring, a rotary cover, and a base. The casing is provided with a plurality of retaining holes and retaining projections. The seat ring is located in the top of a cylindrical object which is formed by the casing. The base if disposed at the bottom of the cylindrical object. The rotary cover is provided with a plurality of retaining protrusions. The seat ring is provided with a plurality of locating slots. The rotary cover is located by the seat ring such that the retaining protrusions of the rotary cover are located in the locating slots of the seat ring.

Abstract: A combined pen and tool arrangement includes a lower penholder holding an ink cartridge for writing, an upper penholder fastened to the lower penholder, and a tool holder mounted inside the upper penholder and holding a pair of scissors and a cutter. The scissors and the cutter are respectively turned in and out of the tool holder and the upper penholder through a longitudinal slot in the tool holder and a longitudinal slot in the upper penholder.

Abstract: A round knife including a handle which is provided in a head end thereof with a slot for receiving pivotally a round knife blade and a support frame. The slot is provided with a protective groove for retaining and locating the support frame. When the support frame is securely engaged with the protective groove, the round knife blade is concealed securely by a protective shield of the support frame. The support frame can be actuated by an actuation piece to rotate so as to expose the round knife blade to execute the cutting operation.

Abstract: A printing head structure of calculator, including a belt type printing head the outer periphery of which is disposed with at least one group of fine characters and at least one group of coarse characters. The fine characters have the same symbols and numerals as the coarse ones, while having different thicknesses and letterforms. By means of a printing control program of the calculator, the printing head is able to print out a positive or negative result respectively by fine characters or coarse characters so as to apparently visually distinguish the positive result from the negative one and thus achieve a reliably reminding effect.