A Method of Gene-Function Annotation Based on Variable Precision Rough Sets

A Method of Gene-Function Annotation Based on Variable Precision Rough Sets

Zhi-li Pei^1,2, Xiao-hu Shi¹, Meng Niu¹, Xu-ning Tang³, Li-sha Liu¹, Ying Kong⁴ ,Yan-chun Liang¹

1. College of Computer Science and Technology, Jilin University, Key Laboratory of Symbol Computation and
Knowledge Engineering of the Ministry of Education, Changchun, 130012, P. R. China
2. College of Mathematics and Computer Science, Inner Mongolia University for Nationalities,
Tongliao 028043, P. R. China
3. College of Software, Jilin University, Changchun, 130012, P. R. China
4. Department of Biochemistry and Molecular Biology, Institution of Glycobiology,
Dalian Medical University, Dalian, 116027, P. R. China

Received:2007-06-30 Revised:2007-07-28 Online:2007-09-30 Published:2007-07-28
Contact: Yan-chun Liang

Abstract

Abstract: It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.

Key words: gene function, annotation, variable precision rough set, GO, BLAST

Zhi-li Pei^1,2, Xiao-hu Shi¹, Meng Niu¹, Xu-ning Tang³, Li-sha Liu¹, Ying Kong⁴ ,Yan-chun Liang¹. A Method of Gene-Function Annotation Based on Variable Precision Rough Sets
[J].J4, 2007, 4(3): 177-184.

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