Document Type

Journal Article

Department/Unit

Department of Computer Science

Title

A private DNA motif finding algorithm

Language

English

Abstract

With the increasing availability of genomic sequence data, numerous methods have been proposed for finding DNA motifs. The discovery of DNA motifs serves a critical step in many biological applications. However, the privacy implication of DNA analysis is normally neglected in the existing methods. In this work, we propose a private DNA motif finding algorithm in which a DNA owner's privacy is protected by a rigorous privacy model, known as {small element of}- differential privacy. It provides provable privacy guarantees that are independent of adversaries' background knowledge. Our algorithm makes use of the n-gram model and is optimized for processing large-scale DNA sequences. We evaluate the performance of our algorithm over real-life genomic data and demonstrate the promise of integrating privacy into DNA motif finding. © 2014 Elsevier Inc.

Keywords

Motif finding, N-gram model, Privacy protection, {small element of}-Differential privacy

Publication Date

2014

Source Publication Title

Journal of Biomedical Informatics

Volume

50

Start Page

122

End Page

132

Publisher

Elsevier

DOI

10.1016/j.jbi.2013.12.016

Link to Publisher's Edition

http://dx.doi.org/10.1016/j.jbi.2013.12.016

ISSN (print)

15320464

ISSN (electronic)

15320480

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