Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract: The present invention provides mutant DNA polymerases, polynucleotides encoding the polymerases, cassettes and vectors including such polynucleotides, and cells containing the polymerases, polynucleotides, cassettes, and/or vectors of the invention. The present invention also provides methods for synthesizing polynucleotides and kits including a DNA polymerase of the invention.

Abstract: Disclosed are assays, methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from complex food matrices, water, a beverage sample, a fermentation broth, a forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract: Disclosed are methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from samples such as: complex food matrices, water, beverages, fermentation broths, forensic & biological samples, and environmental samples including food processing and manufacturing surfaces. In some embodiments, a method of the disclosure comprises: hybridizing at least a first pair of polynucleotide primers to at least a first target polynucleotide sequence, hybridizing at least a second pair of polynucleotide primers to at least a second target polynucleotide sequence, amplifying the at least first and at least second target polynucleotide sequences, and detecting the first and second amplified target polynucleotide sequence products, wherein the detection of both the first amplified target polynucleotide sequence product and the second amplified target polynucleotide sequence product is indicative of the presence of E. coli O157:H7 in a sample and not E. coli O55:H7.

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract: Disclosed are assays, methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from complex food matrices, water, a beverage sample, a fermentation broth, a forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.

Abstract: Disclosed are primer and probe compositions, PCR assays, methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from a variety of samples. In some embodiments, methods for specifically detecting E. coli O157:H7 comprise: hybridizing at least a first pair of polynucleotide primers to at least a first target polynucleotide sequence, hybridizing at least a second pair of polynucleotide primers to at least a second target polynucleotide sequence, amplifying said at least first and said at least second target polynucleotide sequences, and detecting said at least first and said at least second amplified target polynucleotide sequence products, wherein the detection of both the first amplified target polynucleotide sequence product and the second amplified target polynucleotide sequence product is indicative of the presence of E. coli O157:H7 in a sample and not E. coli O55:H7.

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.

Abstract: Disclosed is the genomic sequence for E. coli O55:H7 as well as compositions, methods, and kits for detecting, identifying and distinguishing E. coli O55:H7 from non-O55:H7 strains. In some embodiments, isolated nucleic acid compositions unique and/or specific to E. coli O55:H7 are described. Methods of detection and/or indentifying E. coli O55:H7 comprising detecting at least one nucleic acid sequences comprising or derived from SEQ ID NO:1-5, SEQ ID NO: 66, SEQ ID NO: 252, SEQ ID NO: 1113, and SEQ ID NO: 1461, are described. Primer and probe compositions and methods of use of primers and probes are also provided. Kits for identification of E. coli O55:H7 are also described.

Abstract: The present invention provides mutant DNA polymerases, polynucleotides encoding the polymerases, cassettes and vectors including such polynucleotides, and cells containing the polymerases, polynucleotides, cassettes, and/or vectors of the invention. The present invention also provides methods for synthesizing polynucleotides and kits including a DNA polymerase of the invention.

Abstract: Disclosed are assays, methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from complex food matrices, water, a beverage sample, a fermentation broth, a forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.

Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.

Abstract: The teachings herein generally relates to probes comprising fabricated coded molecular tags for detecting analytes. The teachings also relate to compositions, methods, and kits for fabricating coded molecular tags comprising a multiplicity or reporter groups in an ordered pattern.

Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.

Abstract: The invention provides novel dye-labeled ribonucleotide analogs and methods for synthesizing those analogs. The compounds of the invention are especially useful for DNA sequencing by the polymerase chain reaction.