Performance evaluation of a database of repetitive elements in complete genomes

Jong Tzong Horng; Feng Mao Lin; Li Cheng Wu; Chia Hui Chang

doi:10.1016/j.jss.2003.08.244

Performance evaluation of a database of repetitive elements in complete genomes

Jong Tzong Horng, Feng Mao Lin, Li Cheng Wu, Chia Hui Chang

Research output: Contribution to journal › Article › peer-review

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). http://rsdb.csie.ncu.edu.tw/¹ 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.

Original language	English
Pages (from-to)	491-506
Number of pages	16
Journal	Journal of Systems and Software
Volume	73
Issue number	3
DOIs	https://doi.org/10.1016/j.jss.2003.08.244
State	Published - Nov 2004

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10.1016/j.jss.2003.08.244

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title = "Performance evaluation of a database of repetitive elements in complete genomes",

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). http://rsdb.csie.ncu.edu.tw/1 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.",

author = "Horng, {Jong Tzong} and Lin, {Feng Mao} and Wu, {Li Cheng} and Chang, {Chia Hui}",

note = "Funding Information: The authors would like to thank Li-Wei Liu for his providing the infrastructure of RSDB and Hu-Chia Chang for his implementation of experiments of distributed RSDB. The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC-92-2213-E-008-005. The authors are grateful to Prof. Cheng-Yuan Kao for his contribution to this research. ",

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AU - Lin, Feng Mao

AU - Wu, Li Cheng

AU - Chang, Chia Hui

N1 - Funding Information: The authors would like to thank Li-Wei Liu for his providing the infrastructure of RSDB and Hu-Chia Chang for his implementation of experiments of distributed RSDB. The authors would like to thank the National Science Council of the Republic of China for financially supporting this research under Contract No. NSC-92-2213-E-008-005. The authors are grateful to Prof. Cheng-Yuan Kao for his contribution to this research.

PY - 2004/11

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N2 - 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). http://rsdb.csie.ncu.edu.tw/1 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.

AB - 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). http://rsdb.csie.ncu.edu.tw/1 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.

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Performance evaluation of a database of repetitive elements in complete genomes

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