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A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment

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Abstract

The nested arc-annotation of a sequence is an important model used to represent structural information for RNA and protein sequences. Given two sequences S1 and S2 and a nested arc-annotation P1 for S1, this paper considers the problem of inferring the nested arc-annotation P2 for S2 such that (S1, P1) and (S2, P2) have the largest common substructure. The problem has a direct application in predicting the secondary structure of an RNA sequence given a closely related sequence with known secondary structure. The currently most efficient algorithm for this problem requires O(nm3) time and O(nm2) space where n is the length of the sequence with known arc-annotation and m is the length of the sequence whose arc-annotation is to be inferred. By using sparsification on a new recursive dynamic programming algorithm and applying a Hirschberg-like traceback technique with compression, we obtain an improved algorithm that runs in min{O(nm2 + n2m),O(nm2 log n), O(nm3)} time and min{O(m2 + mn), O(m2 log n + n)} space.

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Authors and Affiliations

  1. Department of Computer Science, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore

    Jesper Jansson, Wing-Kin Sung & Hugo Willy

  2. Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore

    See-Kiong Ng

  3. Genome Institute of Singapore, Genome #02-01, 60 Biopolis Street, Singapore 138672, Singapore

    Wing-Kin Sung

Authors
  1. Jesper Jansson
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  2. See-Kiong Ng
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  3. Wing-Kin Sung
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  4. Hugo Willy
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Corresponding authors

Correspondence to Jesper Jansson, See-Kiong Ng, Wing-Kin Sung or Hugo Willy.

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Jansson, J., Ng, SK., Sung, WK. et al. A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment. Algorithmica 46, 223–245 (2006). https://doi.org/10.1007/s00453-006-1207-0

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  • DOI: https://doi.org/10.1007/s00453-006-1207-0

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