生物信息导论英文论文Practical Suffix Tree Construction 生物信息导论英文论文_Practical Suffix Tree Construction.docVIP

Practical Suffix Tree Construction Sandeep Tata Richard A. Hankins Jignesh M. Patel University of Michigan Abstract Large string datasets are common in a number of emerging text and biological database applications. Common queries over such datasets include both exact and approximate string matches. These queries can be evaluated very efficiently by using a suffix tree index on the string dataset. Although suffix trees can be constructed quickly in memory for small input datasets, constructing persistent trees for large datasets has been challenging. In this paper, we explore suffix tree construction algorithms over a wide spectrum of data sources and sizes. First, we show that on modern processors, a cache-efficient algorithm with O(n2) complexity outperforms the popular O(n) Ukkonen algorithm, even for in-memory construction. For larger datasets, the disk I/O requirement quickly becomes the bottleneck in each algorithm’s performance. To address this problem, we present a buffer management strategy for the O(n2) algorithm, creating a new disk-based construction algorithm that scales to sizes much larger than have been previously described in the literature. Our approach far outperforms the best known diskbased construction algorithms. 1 Introduction Querying large string datasets is becoming increasingly important in a number of emerging text and life sciences applications. Life science researchers are often interested in explorative querying of large biological sequence databases, such as genomes and large sets of protein sequences. Many of these biological datasets are growing at exponential rates — for example, the sizes of the sequence datasets in GenBank have been doubling every six- Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by perm