QUASAR:一种生物序列数据库的搜索算法

doi:10.11925/infotech.1003-3513.2006.04.18

现代图书情报技术

2006, Vol. 1

Issue (4): 74-76 https://doi.org/10.11925/infotech.1003-3513.2006.04.18

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QUASAR:一种生物序列数据库的搜索算法

喻钧¹ 胡志毅² 王建国¹

¹ (西安工业学院计算机科学与工程学院西安 710032)
² (总后建筑工程研究所西安 710032）

QUASAR: An Algorithm for Searching Biological Sequence Databases

Yu Jun¹Hu Zhiyi²Wang Jianguo¹

¹(School of Computer Science and Engineering, Xi’an Institute of Technology, Xi’an 710032,China)
²(Architectural Engineering Institute of the General Logistics Department, Xi’an 710032, China)

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摘要

介绍一种生物序列数据库的搜索算法——QUASAR，即采用索引的后缀数组，通过筛选q-gram进行局部比对的方式来搜索查询序列在数据库中的近似匹配，并运用窗口推移和分块查找的方法来加快搜索和节省搜索空间。同时，将QUASAR和最流行的BLAST搜索工具进行简单比较。

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关键词 ：生物序列数据库, QUASAR, 数据搜索

Abstract：

This paper introduces an algorithm for searching biological sequence databases——QUASAR. It is based on an index suffix array, as well as uses qgram filtration and local alignment to search approximate matches of a query sequence in the databases. And also uses Window shifting and block addressing in order to speed up the retrieval and reduce the space. Finally, compares QUASAR with BLAST which is a popular searching algorithm currently.

Key words： Biological sequence databases QUASAR Databases searching

收稿日期: 2006-01-23 出版日期: 2006-04-25

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通讯作者: 喻钧 E-mail: jyu0117@163.com

作者简介: 喻钧,胡志毅,王建国

引用本文:

喻钧,胡志毅,王建国 . QUASAR:一种生物序列数据库的搜索算法[J]. 现代图书情报技术, 2006, 1(4): 74-76.
Yu Jun,Hu Zhiyi,Wang Jianguo . QUASAR: An Algorithm for Searching Biological Sequence Databases. New Technology of Library and Information Service, 2006, 1(4): 74-76.

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https://manu44.magtech.com.cn/Jwk_infotech_wk3/CN/10.11925/infotech.1003-3513.2006.04.18 或 https://manu44.magtech.com.cn/Jwk_infotech_wk3/CN/Y2006/V1/I4/74

1Cyntbia Gibas, Per Jambeck. Developing Bioinformatics Computer Skills. O’Reilly, 2002
2G.Myers, R.Durbin. Accelerating SmithWaterman Searches. LNCS Vol.2452:331-342, Springer, 2002
3F.Galisson, The Fasta and BLAST programs, Manuscript , 2000
4S.Burkhardt, A.Crauser,P.Ferragina, etal. Q-gram Based Databases Searching Using a Suffix Array (QUASAR). Proc. RECOMB(99): 77-83, ACM press, 1999
5WingKin Sung. Searching biological database . (2005-08). http://www.comp.nus.edu.sg/~ksung/cs5238/note/Lect3-database_2005.pdf(Accessed Dec.8,2005)

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