利用压缩编码提高FM-Index的向后搜索吞吐量

2019 Data Compression Conference (DCC) Pub Date : 2019-03-01 DOI:10.1109/DCC.2019.00089

Jose M. Herruzo, S. González-Navarro, P. Ibáñez, V. Viñals, Jesús Alastruey-Benedé, O. Plata

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引用次数: 0

摘要

DNA测序技术的快速发展要求压缩数据结构以支持快速的模式匹配查询。FM-index是一种广泛使用的压缩数据结构，它还支持快速模式匹配查询。精确匹配算法通常受内存约束，导致性能较差。我们提出了一种新的FM-index数据布局，它压缩了执行搜索过程所需的所有数据。这使得基因组数据的搜索计算时间得到了改善。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Boosting Backward Search Throughput for FM-Index Using a Compressed Encoding

The rapid development of DNA sequencing technologies has demanded for compressed data structures supporting fast pattern matching queries. FM-index is a widely-used compressed data structure that also supports fast pattern matching queries. It is common for the exact matching algorithm to be memory bound, resulting in poor performance. We propose a new data-layout of FM-index that compacts all data needed to perform the searching process. This results in an improvement of the search computing time for genomic data.

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2019 Data Compression Conference (DCC)

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