License: 
Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2018.21
URN: urn:nbn:de:0030-drops-93236
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2018/9323/
Alzamel, Mai ;
Ayad, Lorraine A. K. ;
Bernardini, Giulia ;
Grossi, Roberto ;
Iliopoulos, Costas S. ;
Pisanti, Nadia ;
Pissis, Solon P. ;
Rosone, Giovanna
Degenerate String Comparison and Applications
Abstract
A generalised degenerate string (GD string) S^ is a sequence of n sets of strings of total size N, where the ith set contains strings of the same length k_i but this length can vary between different sets. We denote the sum of these lengths k_0, k_1,...,k_{n-1} by W. This type of uncertain sequence can represent, for example, a gapless multiple sequence alignment of width W in a compact form. Our first result in this paper is an O(N+M)-time algorithm for deciding whether the intersection of two GD strings of total sizes N and M, respectively, over an integer alphabet, is non-empty. This result is based on a combinatorial result of independent interest: although the intersection of two GD strings can be exponential in the total size of the two strings, it can be represented in only linear space. A similar result can be obtained by employing an automata-based approach but its cost is alphabet-dependent. We then apply our string comparison algorithm to compute palindromes in GD strings. We present an O(min{W,n^2}N)-time algorithm for computing all palindromes in S^. Furthermore, we show a similar conditional lower bound for computing maximal palindromes in S^. Finally, proof-of-concept experimental results are presented using real protein datasets.
BibTeX - Entry
@InProceedings{alzamel_et_al:LIPIcs:2018:9323,
author = {Mai Alzamel and Lorraine A. K. Ayad and Giulia Bernardini and Roberto Grossi and Costas S. Iliopoulos and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone},
title = {{Degenerate String Comparison and Applications}},
booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
pages = {21:1--21:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-082-8},
ISSN = {1868-8969},
year = {2018},
volume = {113},
editor = {Laxmi Parida and Esko Ukkonen},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address = {Dagstuhl, Germany},
URL = {http://drops.dagstuhl.de/opus/volltexte/2018/9323},
URN = {urn:nbn:de:0030-drops-93236},
doi = {10.4230/LIPIcs.WABI.2018.21},
annote = {Keywords: degenerate strings, generalised degenerate strings, elastic-degenerate strings, string comparison, palindromes}
}
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Keywords: |
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degenerate strings, generalised degenerate strings, elastic-degenerate strings, string comparison, palindromes |
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Collection: |
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18th International Workshop on Algorithms in Bioinformatics (WABI 2018) |
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Issue Date: |
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2018 |
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Date of publication: |
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02.08.2018 |
