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

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.