Spaced Seed Optimization

Karami, Moein; Zentgraf, Jens; Rahmann, Sven

doi:10.4230/artifacts.27677

Artifact

Spaced Seed Optimization Software

Authors Moein Karami , Jens Zentgraf , Sven Rahmann

Part of: Collection: Supplementary Materials
License: MIT License
Publication Date: 2026-08-27

Document Identifiers

DOI: 10.4230/artifacts.27677
URN: urn:nbn:de:0030-drops-276776

Author Details

Moein Karami

Algorithmic Bioinformatics, Faculty of Mathematics and Computer Science, Saarland University, Saarbrücken, Germany
Center for Bioinformatics Saar, Saarland Informatics Campus, Saarbrücken, Germany
Saarbrücken Graduate School of Computer Science, SIC, Saarbrücken, Germany

Jens Zentgraf

Algorithmic Bioinformatics, Faculty of Mathematics and Computer Science, Saarland University, Saarbrücken, Germany
Center for Bioinformatics Saar, Saarland Informatics Campus, Saarbrücken, Germany
Saarbrücken Graduate School of Computer Science, SIC, Saarbrücken, Germany

Sven Rahmann

Algorithmic Bioinformatics, Faculty of Mathematics and Computer Science, Saarland University, Saarbrücken, Germany
Center for Bioinformatics Saar, Saarland Informatics Campus, Saarbrücken, Germany

Content

Software (Source code): https://gitlab.com/rahmannlab/seed-optimization/
archived version

Version/Status

Content created at: 2026-07-01
Status: Active (at the time of publication 2026-08-27)

Cite As Get BibTex

Moein Karami, Jens Zentgraf, Sven Rahmann. Spaced Seed Optimization (Software, Source code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026) https://doi.org/10.4230/artifacts.27677

Description

This repository contains software that accompanies papers "Designing Exact Spaced Seed Filters Based on Combined Hit and Coverage Information" (WABI 2025) and "Design of Worst-Case-Optimal Spaced Seeds" (WABI 2026).

Subject Classification

Keywords

spaced seeds
gapped k-mers
gapped q-grams

Programming Languages

Python
numba

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