Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications

Solon Pissis, Ahmad Retha
<span title="">2015</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="" style="color: black;">2015 IEEE International Parallel and Distributed Processing Symposium Workshop</a> </i> &nbsp;
Approximate string matching is the problem of finding all factors of a text t of length n with a distance at most k from a pattern x of length m ≤ n. Fixed-length approximate string matching is the problem of finding all factors of a text t of length n with a distance at most k from any factor of length h of a pattern x of length m ≤ n, where h ≤ m. It is thus a generalisation of approximate string matching and has numerous direct applications in molecular biology-motif extraction and circular
more &raquo; ... equence alignment, to name a few. MaxShiftM is a bit-parallel algorithm for fixed-length approximate string matching under the Hamming distance model with time complexity O(m h/w n), where w is the size of the computer word (Crochemore et al., 2010) . An implementation of this algorithm is straightforward as long as the maximal length of alignments is less than or equal to w. In this article, our contribution is twofold: first, we propose a generalised implementation of MaxShiftM, that is, for any given h ≤ m, under the Hamming distance model; and second, we show how our implementation can be used to improve the accuracy and efficiency of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1109/ipdpsw.2015.106</a> <a target="_blank" rel="external noopener" href="">dblp:conf/ipps/PissisR15</a> <a target="_blank" rel="external noopener" href="">fatcat:ttxri4mxtbbdzm5gni6d6p2kra</a> </span>
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