Indexing a sequence for mapping reads with a single mismatch

Author:

Crochemore Maxime12,Langiu Alessio13,Rahman M. Sohel14

Affiliation:

1. Department of Informatics, King's College London, London WC2R 2LS, UK

2. Laboratoire d'informatique Gaspard-Monge, Université Paris-Est, Paris, France

3. Department of Mathematics and Informatics, University of Palermo, Palermo, Italy

4. AℓEDA Group, Department of CSE, BUET, Dhaka-1000, Bangladesh

Abstract

Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the sequence, m is the length of the read, 0< ε <1 and is the optimal output size.

Publisher

The Royal Society

Subject

General Physics and Astronomy,General Engineering,General Mathematics

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Longest Common Prefix with Mismatches;String Processing and Information Retrieval;2015

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