Patent · US Active

Efficient genomic read alignment in an in-memory database

US10381106B2 · kind B2 · utility

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20Claims

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Assignee

Hasso-Plattner Institut fuer Softwaresystemtechnik GmbH · DE

Inventors

Hasso Plattner · Schriesheim, DE
Matthieu-Patrick Schapranow · Berlin, DE
Emanuel Ziegler · Heidelberg, DE

Key dates

Filing date	Jan 27, 2014
Grant date	Aug 13, 2019
Priority date	—
Expiry date	Mar 21, 2036

Classification

Technology area (CPC G)Physics
CPC primaryG16B45/00
WIPO fieldComputer technology
WIPO sectorElectrical engineering

Abstract

A high performance, low-cost, gapped read alignment algorithm is disclosed that produces high quality alignments of a complete human genome in a few minutes. Additionally, the algorithm is more than an order of magnitude faster than previous approaches using a low-cost workstation. The results are obtained via careful algorithm engineering of the seeding based approach. The use of non-hashed seeds in combination with techniques from search engine ranking achieves fast cache-efficient processing. The algorithm can also be efficiently parallelized. Integration into an in-memory database infrastructure (IMDB) leads to low overhead for data management and further analysis.

Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.