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| 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) |
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Abstract 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.
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Received: 23 January 2006
Published: 25 April 2006
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Corresponding Authors:
Yu Jun
E-mail: jyu0117@163.com
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| About author:: Yu Jun,Hu Zhiyi,Wang Jianguo |
| 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) |
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