公开(公告)号：US20200051663A1

公开(公告)日：2020-02-13

申请号：US16279315

申请日：2019-02-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Zheng ZHANG ,  Danwei GUO ,  Yuandan LOU ,  Asim SIDDIQUI ,  Dumitru BRINZA

IPC: G16B30/00

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

公开(公告)号：US20160333401A1

公开(公告)日：2016-11-17

申请号：US15099685

申请日：2016-04-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Heinz BREU ,  Danwei GUO

IPC: C12Q1/68 ,  G06F19/22

CPC classification number: C12Q1/6869 ,  G16B30/00 ,  C12Q2535/131 ,  C12Q2565/1025

Abstract: Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.

Abstract translation: 公开了使用颜色调用重新测序的系统和方法。 DNA样本根据多基因码进行编码和测序，产生样本片段的一系列读取颜色调用。 得到参考序列。 读取颜色调用的字符串映射到参考序列。 从参考序列中提取碱基序列。 基本序列根据多基本码被编码为参考颜色码串。 读取颜色调用的字符串与参考颜色代码的字符串对齐，并且检测到对齐中的不匹配。 读取颜色调用字符串的一个或多个不匹配被注释为不一致。 读取颜色调用串的一个或多个不一致的不匹配被更正。 将经校正的读取颜色调用的字符串解码为产生读取序列的基准。