Performance evaluation of a database of repetitive elements in complete genomes

Authors:
Jong-Tzong Horng;Feng-Mao Lin;Li-Cheng Wu;Chia-Hui Chang
Affiliations:
Department of Computer Science and Information Engineering, National Central University, Jungli 320, Taiwan;Department of Computer Science and Information Engineering, National Central University, Jungli 320, Taiwan;Department of Computer Science and Information Engineering, National Central University, Jungli 320, Taiwan;Department of Computer Science and Information Engineering, National Central University, Jungli 320, Taiwan
Venue:
Journal of Systems and Software
Year:
2004

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The VLDB Journal — The International Journal on Very Large Data Bases

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Abstract

The analysis of repetitive elements reveals repetitive elements in our genome may have been very important in the evolutionary genomics. In this work, we propose approaches to improve the performance of the repetitive elements in a database, namely Repetitive Sequence Database (RSDB). There are hundreds of millions of repetitive elements in RSDB. Performance evaluation and tuning are critical for us to manage such a large database. Not only does this study have a lot of performance improvements on centralized RSDB, but also this study provides a comparison of performance between centralized RSDB and distributed RSDB. From the experimental results, we find the improvements proposed speed up our RSDB very much.