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Linear-space algorithms that build local alignments from fragments

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Abstract

This paper presents practical algorithms for building an alignment of two long sequences from a collection of “alignment fragments,” such as all occurrences of identical 5-tuples in each of two DNA sequences. We first combine a time-efficient algorithm developed by Galil and coworkers with a space-saving approach of Hirschberg to obtain a local alignment algorithm that uses0((M+N+F logN) logM) time and0(M+N) space to align sequences of lengthsM andN from a pool of F alignment fragments. Ideas of Huang and Miller are then employed to develop a time- and space-efficient algorithm that computesn best nonintersecting alignments for anyn>1. An example illustrates the utility of these methods.

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Authors and Affiliations

  1. Department of Computer Science, The Pennsylvania State University, 16802, University Park, PA, USA

    Kun -Mao Chao & W. Miller

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  1. Kun -Mao Chao
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  2. W. Miller
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Additional information

Communicated by E. W. Myers.

This work was supported in part by Grant RO1 LM05110 from the National Library of Medicine.

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Chao, K.M., Miller, W. Linear-space algorithms that build local alignments from fragments. Algorithmica 13, 106–134 (1995). https://doi.org/10.1007/BF01188583

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  • DOI: https://doi.org/10.1007/BF01188583

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