Repeats identification using improved suffix trees. (11th December 2009)

• Record Type: Journal Article
• Authors: Huo, Hongwei; Wang, Xiaowu; Stojkovic, Vojislav
• Is Part Of: International journal of computational biology and drug design. Volume 2:Number 3(2009)
• Page Start: 264
• Page End: 277
• Publication Date: 2009-12-11
• Subjects: repeats identification -- improved suffix trees -- RepSeeker algorithm -- suffix tree data structure -- bioinformatics -- gene sequences; Computational biology -- Periodicals; Drugs -- Design -- Periodicals; 570.285
• Languages: English
• ISSNs: 1756-0756

Abstract

The suffix tree data structure plays an important role in the efficient implementations of some querying algorithms. This paper presents the fast Rep(eats)Seeker algorithm for repeats identification based on the improvements of suffix tree construction. The leaf nodes and the branch nodes are numbered in different ways during the construction of a suffix tree and extra information is added to the branch nodes. The experimental results show that improvements reduce the running time of the RepSeeker algorithm without losing the accuracy. The experimental results coincide with the theoretical expectations.