NDLI: An Adaptive Suffix Tree Based Algorithm for Repeats Recognition in a DNA Sequence

Content Provider	IEEE Xplore Digital Library
Author	Hongwei Huo Xiaowu Wang Stojkovic, V.
Copyright Year	2009
Abstract	Many methods for repeats recognition are based on alignments. Their speed and time significantly limit their applications. This paper presents the fast Rep(eats)Seeker algorithm for repeats recognition based on the adaptive Ukkonen algorithm for a suffix tree construction. The RepSeeker algorithm uses the lowest frequency limit to maximize the extension of repeats. The adaptive improvements to the Ukkonen suffix tree construction are made to increase the efficiency of the RepSeeker algorithm. The node information required by the RepSeeker algorithm is added during the suffix tree construction. Because information in leaves and branch nodes are different, the RepSeeker algorithm directly obtains the needed information from nodes to find out the frequency and locate the positions of the substring. The improvement is noticeable for the repeats recognition. Comparisons between before and after improvements of the suffix tree construction show that improvements greatly reduce the running time of the RepSeeker algorithm without losing the accuracy.
Starting Page	181
Ending Page	184
File Size	1013564
Page Count	4
File Format	PDF
ISBN	9780769537399
DOI	10.1109/IJCBS.2009.65
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-08-03
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences adaptive suffix tree Genomics Humans Ukkonen algorithm RepSeeker algorithm Diseases Computer science Systems biology DNA Frequency Libraries Bioinformatics Repeats recognition
Content Type	Text
Resource Type	Article

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