Efficient Interval Query of Genome Alignment and Interval Databases in Cloud Environment

Abstract

Interval overlap query has become a fundamental tool for biomedical researches. However, existing methods are either not efficient or hardly to extend. In this paper, cloud computing is applied to solving the limited speed and scalability problems of interval overlap query. First, the NCList algorithm based on centralized environment is applied to cloud computing in order to improve the query efficiency, and the CNCList algorithm is presented. Second, two optimization strategies are proposed to further enhance the query efficiency of CNCList and an advanced algorithm named CNCList⁺ is formed. Third, detailed comparison experiments between CNCList⁺ and CNCList prove the better performance of CNCList⁺ both on query time and scalability, thus demonstrating the excellent capability of CNCList⁺ on solving the limited query speed and scalability problems of interval overlap query.