Life Technologies Corporation

Applera Corporation

Yuandan Lou

Asim Siddiqui

Jon M Sorenson

Dumitru Brinza

Kai C Yung

Sylvia H Fang

Zheng Zhang

Heinz Breu

Puneet Suri

Amitabh Shukla

Danwei Guo

Brijesh Krishnaswami

Karl Kuhlmann

Catherine E Frantz

Thomas E Birkett

Salil Kumar

Benjamin B Jones

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.

Systems and methods for analyzing nucleic acid sequences

Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

Systems and methods for analysis and interpretation of nucliec acid sequence data

An automated system for evaluating biological samples which includes a centralized registry that contains protocols and configuration information for both instruments and analysis applications. The registry provides for improved automation of biological process runs using an autoanalysis applications manager component or daemon, which accesses and transmits the appropriate protocol and configuration information to selected instruments and/or applications. This information is used to instruct data capture by the biological instruments and direct the analysis of the data by the analysis applications.

Auto-analysis framework for sequence evaluation

Growing community of inventors

Cupertino, CA, United States of America

Yuandan Lou