SMART: SuperMaximal approximate repeats tool
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Updated: Aug 3, 2026
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Lorraine A K Ayad1, Panagiotis Charalampopoulos1,2, Solon P Pissis3
1Department of Informatics, King's College London, London, UK.
Summary:
State-of-the-art repeat analysis tools rely on extending maximal repeated pairs to enumerate maximal k-mismatch repeats. These pairs can be quadratic in n, the length of the input sequence, and thus greedy heuristics are applied to speed up the extension. Here, we introduce supermaximal k-mismatch repeats, which are linear in n and capture all maximal k-mismatch repeats: every maximal k-mismatch repeat is a substring of some supermaximal k-mismatch repeat. We present SMART, a tool based on recent algorithmic advances implemented in C++ to compute supermaximal k-mismatch repeats directly, and show that these elements are statistically much more significant than the output of the state-of-the-art.
Availability And Implementation:
http://github.com/lorrainea/smart (GNU GPL v3.0).
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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