Moein Karami, Jens Zentgraf, Sven Rahmann. Spaced Seed Optimization (Software, Source code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)
@misc{dagstuhl-artifact-27677,
title = {{Spaced Seed Optimization}},
author = {Karami, Moein and Zentgraf, Jens and Rahmann, Sven},
note = {Software, version 0.11., swhId: \href{https://archive.softwareheritage.org/swh:1:dir:050c8caccda68021f2feb9b7b8400444e9888340;origin=https://gitlab.com/rahmannlab/seed-optimization;visit=swh:1:snp:ed60ba2d5efcd8199c1bf281817a561772cb5d47;anchor=swh:1:rev:61d973045b71d7ec0c3bc2ef40bd7db39f485748}{\texttt{swh:1:dir:050c8caccda68021f2feb9b7b8400444e9888340}} (visited on 2026-08-27)},
url = {https://gitlab.com/rahmannlab/seed-optimization/},
doi = {10.4230/artifacts.27677},
}
Published in: LIPIcs, Volume 390, 26th International Conference on Algorithms for Bioinformatics (WABI 2026)
Moein Karami, Jens Zentgraf, and Sven Rahmann. Designing Exact Spaced Seed Filters Based on Combined Hit and Coverage Information. In 26th International Conference on Algorithms for Bioinformatics (WABI 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 390, pp. 21:1-21:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)
@InProceedings{karami_et_al:LIPIcs.WABI.2026.21,
author = {Karami, Moein and Zentgraf, Jens and Rahmann, Sven},
title = {{Designing Exact Spaced Seed Filters Based on Combined Hit and Coverage Information}},
booktitle = {26th International Conference on Algorithms for Bioinformatics (WABI 2026)},
pages = {21:1--21:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-446-8},
ISSN = {1868-8969},
year = {2026},
volume = {390},
editor = {El-Mabrouk, Nadia and Vandin, Fabio},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2026.21},
URN = {urn:nbn:de:0030-drops-275252},
doi = {10.4230/LIPIcs.WABI.2026.21},
annote = {Keywords: Spaced seed, Gapped k-mer, Hit, Coverage, Integer linear program (ILP), Dynamic programming (DP), Similarity search}
}