公开(公告)号：US08486630B2

公开(公告)日：2013-07-16

申请号：US12613291

申请日：2009-11-05

申请人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

发明人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

IPC分类号： C12Q1/68

CPC分类号： G06F19/22 ,  C12Q1/6869 ,  C12Q2531/125 ,  C12Q2537/165

摘要： Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

摘要翻译： 本文公开了在具有已知序列的核酸插入物的环状分子中存在的核酸样品中修饰碱基的序列和/或位置的方法，包括获得至少两个插入样品单元的序列数据。 在一些实施方案中，所述方法包括使用环状双锁定分子获得序列数据。 在一些实施方案中，所述方法包括通过将序列与核酸插入物的已知序列进行比较来计算核酸插入序列的分数，以及根据一个或多个核酸插入片段的得分接受或排除核酸样品序列的重复序列 插入物的两个序列紧接着核酸样品序列的重复序列的上游或下游。

公开(公告)号：US08673559B2

公开(公告)日：2014-03-18

申请号：US13492593

申请日：2012-06-08

申请人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

发明人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

IPC分类号： C12Q1/68 ,  G01N33/50

摘要： Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

公开(公告)号：US20120295260A1

公开(公告)日：2012-11-22

申请号：US13492593

申请日：2012-06-08

申请人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

发明人： Chao-Chi Pan ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

IPC分类号： G06F19/22 ,  C12M1/40 ,  C12Q1/68

CPC分类号： G06F19/22 ,  C12Q1/6869 ,  C12Q2531/125 ,  C12Q2537/165

摘要： Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

摘要翻译： 本文公开了在具有已知序列的核酸插入物的环状分子中存在的核酸样品中修饰碱基的序列和/或位置的方法，包括获得至少两个插入样品单元的序列数据。 在一些实施方案中，所述方法包括使用环状双锁定分子获得序列数据。 在一些实施方案中，所述方法包括通过将序列与核酸插入物的已知序列进行比较来计算核酸插入序列的分数，以及根据一个或多个核酸插入片段的得分接受或排除核酸样品序列的重复序列 插入物的两个序列紧接着核酸样品序列的重复序列的上游或下游。

公开(公告)号：US20100121582A1

公开(公告)日：2010-05-13

申请号：US12613291

申请日：2009-11-05

申请人： Chao-Chi PAN ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

发明人： Chao-Chi PAN ,  Jenn-Yeh Fann ,  Chung-Fan Chiou ,  Hung-Chi Chien ,  Hui-Ling Chen

IPC分类号： G06F19/00 ,  C12Q1/68 ,  G01N33/48

CPC分类号： G06F19/22 ,  C12Q1/6869 ,  C12Q2531/125 ,  C12Q2537/165

摘要： Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.

摘要翻译： 本文公开了在具有已知序列的核酸插入物的环状分子中存在的核酸样品中修饰碱基的序列和/或位置的方法，包括获得至少两个插入样品单元的序列数据。 在一些实施方案中，所述方法包括使用环状双锁定分子获得序列数据。 在一些实施方案中，所述方法包括通过将序列与核酸插入物的已知序列进行比较来计算核酸插入序列的分数，以及根据一个或多个核酸插入片段的得分接受或排除核酸样品序列的重复序列 插入物的两个序列紧接着核酸样品序列的重复序列的上游或下游。

公开(公告)号：US09670243B2

公开(公告)日：2017-06-06

申请号：US13117565

申请日：2011-05-27

申请人： Chung-Fan Chiou ,  Chao-Chi Pan ,  Jenn-Yeh Fann ,  Shang-Chia Chang ,  Tsu-Ju Fu

发明人： Chung-Fan Chiou ,  Chao-Chi Pan ,  Jenn-Yeh Fann ,  Shang-Chia Chang ,  Tsu-Ju Fu

IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/04 ,  C07H21/02 ,  C07H19/04

CPC分类号： C07H21/00 ,  C07H21/04 ,  C12Q1/6869 ,  C12Q2525/117 ,  C12Q2525/119 ,  C12Q2565/101

摘要： Embodiments relate to methods of sequencing nucleic acids. Embodiments encompass the use of nucleotide analogs and a nucleic acid polymerase enzyme or enzyme complex comprising proofreading activity. The nucleotide analogs may become incorporated into a replicating strand and induce the proofreading activity of the polymerizing enzyme, thereby prolonging the duration of a signal associated with nucleotide incorporation, resulting in more observable sequencing events and increasing the accuracy of nucleic acid sequencing.

公开(公告)号：US20110300534A1

公开(公告)日：2011-12-08

申请号：US13117565

申请日：2011-05-27

申请人： Chung-Fan Chiou ,  Chao-Chi Pan ,  Jenn-Yeh Fann ,  Shang-Chia Chang ,  Tsu-Ju Fu

发明人： Chung-Fan Chiou ,  Chao-Chi Pan ,  Jenn-Yeh Fann ,  Shang-Chia Chang ,  Tsu-Ju Fu

IPC分类号： C12Q1/68 ,  C07H21/04

CPC分类号： C07H21/00 ,  C07H21/04 ,  C12Q1/6869 ,  C12Q2525/117 ,  C12Q2525/119 ,  C12Q2565/101

摘要： Embodiments relate to methods of sequencing nucleic acids. Embodiments encompass the use of nucleotide analogs and a nucleic acid polymerase enzyme or enzyme complex comprising proofreading activity. The nucleotide analogs may become incorporated into a replicating strand and induce the proofreading activity of the polymerizing enzyme, thereby prolonging the duration of a signal associated with nucleotide incorporation, resulting in more observable sequencing events and increasing the accuracy of nucleic acid sequencing.

摘要翻译： 实施方案涉及核酸测序方法。 实施方案包括使用核苷酸类似物和包含校正活性的核酸聚合酶或酶复合物。 核苷酸类似物可以并入复制链中并诱导聚合酶的校正活性，从而延长与核苷酸掺入相关的信号的持续时间，导致更可观测的测序事件并增加核酸测序的准确性。

公开(公告)号：US20120077274A1

公开(公告)日：2012-03-29

申请号：US12982659

申请日：2010-12-30

申请人： Chung-Fan Chiou ,  Jyh-Chern Chen ,  Ming-Te Lin ,  Chao-Chi Pan ,  Chein-Shiu Kuo ,  Jenn-Yeh Fann

发明人： Chung-Fan Chiou ,  Jyh-Chern Chen ,  Ming-Te Lin ,  Chao-Chi Pan ,  Chein-Shiu Kuo ,  Jenn-Yeh Fann

IPC分类号： G01N35/00 ,  C12M1/34

CPC分类号： G01N15/1056 ,  G01N35/00871 ,  G01N35/1072 ,  G01N2035/0097 ,  Y10T436/11

摘要： A chemical or biochemical analysis apparatus includes: a computer processor; at least one controller electrically coupled to the computer processor; at least one first base configured with a plurality of dispensing tube assemblies arranged in alignment and electrically coupled to the at least one controller, independently; at least one second base configured with a plurality of the detectors arranged in alignment and electrically coupled to the at least one controller; and a stage, for carrying the at least one multi-well strip having a plurality of wells arranged in alignment and for transporting the multi-well strip to pass through and underneath the plurality of dispensing tube assemblies and the plurality of the detectors arranged in order, electrically coupled to the at least one controller.

摘要翻译： 化学或生化分析装置包括：计算机处理器; 至少一个控制器，电耦合到所述计算机处理器; 至少一个第一底座，其配置有多个分配管组件，所述多个分配管组件被排列成对准并电耦合到所述至少一个控制器; 配置有多个检测器的至少一个第二基座布置成对齐并电耦合到所述至少一个控制器; 以及载物台，用于承载至少一个具有排列成对准的多个孔的多孔条，并用于输送多孔条以通过并位于多个分配管组件的下面，并且多个检测器按顺序排列 ，电耦合到所述至少一个控制器。

公开(公告)号：US08223043B2

公开(公告)日：2012-07-17

申请号：US12977457

申请日：2010-12-23

申请人： Bai-Kuang Hwang ,  Jenn-Yeh Fann ,  Chung-Fan Chiou

发明人： Bai-Kuang Hwang ,  Jenn-Yeh Fann ,  Chung-Fan Chiou

IPC分类号： H03M7/30

CPC分类号： G06F19/22

摘要： The invention provides a data compression method, comprising: (a) obtaining a first reading sequence and a second reading sequence from an identical source by a receiving unit; (b) comparing the first reading sequence with the second reading sequence according to a comparison condition to generate a sequence comparison result by the processor; (c) outputting a final template sequence according to the sequence comparison result by the processor; (d) comparing the final template sequence to each of the first and second reading sequences, to generate a respective difference between the final template sequence and each of the first and second reading sequences by the processor; and (e) compressing the first and second reading sequences according to the final template sequences and all generated differences between the final template sequence and the first and second reading sequences, to generate a compression file by the processor.

摘要翻译： 本发明提供了一种数据压缩方法，包括：（a）由接收单元从相同的源获得第一读取序列和第二读取序列; （b）根据比较条件将第一读取序列与第二读取序列进行比较，以生成处理器的序列比较结果; （c）根据处理器的序列比较结果输出最终模板序列; （d）将最终模板序列与第一和第二读取序列中的每一个比较，以由处理器产生最终模板序列与第一和第二读取序列中的每一个之间的相应差异; 和（e）根据最终模板序列压缩第一和第二读取序列以及最终模板序列与第一和第二读取序列之间的所有生成的差异，以由处理器生成压缩文件。

公开(公告)号：US08700340B2

公开(公告)日：2014-04-15

申请号：US12974872

申请日：2010-12-21

申请人： Bai-Kuang Hwang ,  Jenn-Yeh Fann ,  Chao-Chi Pan

发明人： Bai-Kuang Hwang ,  Jenn-Yeh Fann ,  Chao-Chi Pan

IPC分类号： G06F19/00 ,  C12Q1/68 ,  G06F19/22

CPC分类号： G06F19/22 ,  C12Q1/6869

摘要： The invention provides a sequence calibration method, including: (a) obtaining a first reading sequence and a second reading sequence from an identical source by a receiving unit; (b) setting a comparison condition by a determining unit; and (c) comparing the first reading sequence with the second reading sequence according to the comparison condition to generate a sequence comparison result by the determining unit; and (d) outputting a calibrated sequence according to the sequence comparison result by the determining unit, wherein the comparison condition is set according to a first seed table of the first reading sequence and a second seed table of the second reading sequence.

摘要翻译： 本发明提供了一种序列校准方法，包括：（a）由接收单元从相同的源获得第一读取序列和第二读取序列; （b）由确定单元设置比较条件; 和（c）根据比较条件比较第一读取序列与第二读取序列以由确定单元生成序列比较结果; 以及（d）根据所述确定单元的序列比较结果输出经校准的序列，其中根据所述第一读取序列的第一种子表和所述第二读取序列的第二种子表来设置所述比较条件。