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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）
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。
QUASAR: An Algorithm for Searching Biological Sequence Databases
Yu Jun1 Hu Zhiyi2 Wang 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)
This paper introduces an algorithm for searching biological sequence databases——QUASAR. It is based on an index suffix array, as well as uses qgram 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.
G250
1Cyntbia Gibas, Per Jambeck. Developing Bioinformatics Computer Skills. O’Reilly, 2002
2G.Myers, R.Durbin. Accelerating SmithWaterman 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
5WingKin Sung. Searching biological database . (2005-08). http://www.comp.nus.edu.sg/~ksung/cs5238/note/Lect3-database_2005.pdf(Accessed Dec.8,2005)