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1. 发明申请

US20140350866A1 Method of Gap Closing in Nucleotide Sequence and Apparatus Thereof 审中-公开
公开(公告)号：US20140350866A1
公开(公告)日：2014-11-27
申请号：US14361158
申请日：2011-11-29
申请人： Binghang Liu , Zhenyu Li , Yanxiang Chen , Yingrui Li , Jian Wang , Jun Wang , Huanming Yang
发明人： Binghang Liu , Zhenyu Li , Yanxiang Chen , Yingrui Li , Jian Wang , Jun Wang , Huanming Yang
IPC分类号： G06F19/16
CPC分类号： G16B15/00 , C12Q1/6869 , G16B30/00 , C12Q2537/165
摘要： Provided is a method of gap closing in nucleotide sequence. The nucleic acid sequence comprises a first contig at one end of a gap in an unassembled region, and a second contig at the other end of the gap in the unassembled region. The method comprises: selecting reads having an overlap with one end of the first contig close to the gap as a set of reads for gap closing; selecting reads having a shortest overlap with the first contig in the set of reads for gap closing as a candidate read; determining whether reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig present in the set of reads for gap closing, and determining whether reads having no overlapping relationship with the candidate read present in the set of reads for gap closing; obtaining a result of presenting an extension conflict, and determining an unconfident candidate read, if reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig present in the set of reads for gap closing, reads having no overlapping relationship with the candidate read present in the set of reads for gap closing, or both reads having an overlapping length with the first contig shorter than an overlapping length between the candidate read and the first contig, and reads having no overlapping relationship with the candidate read present in the set of reads for gap closing; reselecting the candidate read until obtaining a confident candidate read, if the candidate read is unconfident; connecting the confident candidate read to the first contig, to form a new first contig; determining whether one end of the new first contig close to the gap has an overlap with one end of the second contig close to the gap; performing the step of selecting the set of reads for gap closing on the basis of the new first contig, if the one end of the new first contig close to the gap has no overlap with the one end of the second contig close to the gap, wherein the first contig in the step of selecting the set of reads for gap closing is replaced with the new first contig; connecting the new first contig to the second contig to complete gap closing, if one end of the new first contig close to the gap has an overlap with one end of the second contig close to the gap.

2. 发明授权

US10395757B2 Parental genome assembly method 有权
公开(公告)号：US10395757B2
公开(公告)日：2019-08-27
申请号：US14361865
申请日：2011-12-02
申请人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
发明人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G16B20/00 , C12Q1/6869 , C12Q1/6895 , G16C99/00
摘要： Provided is a parental genome assembly method, comprising: using the sequencing data of parental selfing line progeny population to assemble and perfect the parental genome data. Also provided is a device for implementing the method.

3. 发明申请

US20150205913A1 PARENTAL GENOME ASSEMBLY METHOD 审中-公开
标题翻译：亲本基因组装方法
公开(公告)号：US20150205913A1
公开(公告)日：2015-07-23
申请号：US14361865
申请日：2011-12-02
申请人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
发明人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G06F19/18 , C12Q1/68
CPC分类号： G16B20/00 , C12Q1/6869 , C12Q1/6895 , C12Q2535/122 , G16C99/00
摘要： Provided is a parental genome assembly method, comprising: using the sequencing data of parental selfing line progeny population to assemble and perfect the parental genome data. Also provided is a device for implementing the method.
摘要翻译：提供了一种亲本基因组装配方法，其包括：使用亲本自交系后代群体的测序数据来组合和完善亲本基因组数据。还提供了一种用于实现该方法的装置。

4. 发明申请

US20150120210A1 METHOD AND DEVICE FOR LABELLING SINGLE NUCLEOTIDE POLYMORPHISM SITES IN GENOME 审中-公开
标题翻译：在基因组中标记单个核苷酸多态性位点的方法和装置
公开(公告)号：US20150120210A1
公开(公告)日：2015-04-30
申请号：US14369318
申请日：2011-12-29
申请人： Ye Tao , Zequn Zheng , Zihao Feng , Yingrui Li , Huanming Yang , Jun Wang , Jian Wang
发明人： Ye Tao , Zequn Zheng , Zihao Feng , Yingrui Li , Huanming Yang , Jun Wang , Jian Wang
IPC分类号： G06F19/22
CPC分类号： G16B30/00 , C12Q1/6869 , G16B20/00 , C12Q2535/131
摘要： Disclosed are a method and a device for labelling single nucleotide polymorphism site in a genome. The above-mentioned method comprises: the single-end RAD sequences from the genomes of two individuals are obtained; the single-end RAD sequences are filtered to remove unqualified sequences; the sequencing depth of the sequences from the genomes of two individuals is aligned in pairs and without gaps to determine the SNP sites.
摘要翻译：公开了用于在基因组中标记单核苷酸多态性位点的方法和装置。上述方法包括：获得来自两个个体的基因组的单末端RAD序列; 过滤单端RAD序列以除去不合格序列; 来自两个个体的基因组的序列的测序深度成对排列并且没有间隙以确定SNP位点。

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