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Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.SEA.2018.16
URN: urn:nbn:de:0030-drops-89515
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2018/8951/
Pissis, Solon P. ;
Retha, Ahmad
Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line
Abstract
An elastic-degenerate string is a sequence of n sets of strings of total length N. It has been introduced to represent multiple sequence alignments of closely-related sequences in a compact form. For a standard pattern of length m, pattern matching in an elastic-degenerate text can be solved on-line in time O(nm^2+N) with pre-processing time and space O(m) (Grossi et al., CPM 2017). A fast bit-vector algorithm requiring time O(N * ceil[m/w]) with pre-processing time and space O(m * ceil[m/w]), where w is the size of the computer word, was also presented. In this paper we consider the same problem for a set of patterns of total length M. A straightforward generalization of the existing bit-vector algorithm would require time O(N * ceil[M/w]) with pre-processing time and space O(M * ceil[M/w]), which is prohibitive in practice. We present a new on-line O(N * ceil[M/w])-time algorithm with pre-processing time and space O(M). We present experimental results using both synthetic and real data demonstrating the performance of the algorithm. We further demonstrate a real application of our algorithm in a pipeline for discovery and verification of minimal absent words (MAWs) in the human genome showing that a significant number of previously discovered MAWs are in fact false-positives when a population's variants are considered.
BibTeX - Entry
@InProceedings{pissis_et_al:LIPIcs:2018:8951,
author = {Solon P. Pissis and Ahmad Retha},
title = {{Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line}},
booktitle = {17th International Symposium on Experimental Algorithms (SEA 2018)},
pages = {16:1--16:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-070-5},
ISSN = {1868-8969},
year = {2018},
volume = {103},
editor = {Gianlorenzo D'Angelo},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address = {Dagstuhl, Germany},
URL = {http://drops.dagstuhl.de/opus/volltexte/2018/8951},
URN = {urn:nbn:de:0030-drops-89515},
doi = {10.4230/LIPIcs.SEA.2018.16},
annote = {Keywords: on-line algorithms, algorithms on strings, dictionary matching, elastic-degenerate string, Variant Call Format}
}
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Keywords: |
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on-line algorithms, algorithms on strings, dictionary matching, elastic-degenerate string, Variant Call Format |
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Collection: |
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17th International Symposium on Experimental Algorithms (SEA 2018) |
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Issue Date: |
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2018 |
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Date of publication: |
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19.06.2018 |
