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arXiv · 1704.04615

FMtree: A fast locating algorithm of FM-indexes for genomic data

Haoyu Cheng·Ming Wu·Yun Xu
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Abstract

Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to classical indexes, e.g., suffix trees and suffix arrays, while requiring less space. For genomic data, a well-known family of compressed full-text index, called FM-indexes, presents unmatched performance in practice. One major drawback of FM-indexes is that their locating operations, which report all occurrence positions of patterns in a given text, are particularly slow, especially for the patterns with many occurrences. Results: In this paper, we introduce a novel locating algorithm, FMtree, to fast retrieve all occurrence positions of any pattern via FM-indexes. When searching for a pattern over a given text, FMtree organizes the search space of the locating operation into a conceptual quadtree. As a result, multiple occurrence positions of this pattern can be retrieved simultaneously by traversing the quadtree. Compared with the existing locating algorithms, our tree-based algorithm reduces large numbers of redundant operations and presents better data locality. Experimental results show that FMtree is usually one order of magnitude faster than the state-of-the-art algorithms, and still memory-efficient.

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Haoyu Cheng, Ming Wu, Yun Xu. 2017-04-18. FMtree: A fast locating algorithm of FM-indexes for genomic data. https://arxiv.org/abs/1704.04615

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