Table of Contents 1Introduction1.1Overview 1.2Previous reviews 2Theory of sampling schemes2.1Questions 2.2Types of schemes 2.3Parameter regimes 2.4Different perspectives 2.5UHS vs minimizer scheme 2.6(Asymptotic) bounds 2.7Lower bounds 3Minimizer schemes3.1Orders 3.2UHS-based and search-based schemes 3.3Pure schemes 3.4Other variantsSelection schemes Canonical minimizers 4Open questions 1 Introduction sadf Lots of DNA data Most algorithms deal with k-mers. k-mers overlap, and hence considerin...| Posts on CuriousCoding
Table of Contents Overview Detailed comments Terminology Abstract Preliminaries Methods 3.5 Transformations Results Discussion Comments on “Expected density of random minimizers” These are some (biased) comments on “Greedymini: Generating Low-Density Dna Minimizers” (Golan et al. 2024), which introduces the GreedyMini minimizer scheme. (Meanwhile, this has been published as Golan et al. (2025).) At the bottom, there are also some comment on Golan and Shur (2025).| CuriousCoding
Table of Contents 1 Sampling schemes 1.1 Definitions 1.2 Miniception 1.3 Mod-minimizer 1.4 Forward scheme lower bound 1.5 Open syncmer minimizer 1.6 Open-closed minimizer 1.7 New: General mod-minimizer 1.8 Variant: Open-closed minimizer using offsets 2 Selection schemes 2.1 Definition 2.2 Bd-anchors 2.3 New: Smallest unique substring anchors 2.4 New: Anti lexicographic sorting 3 More sampling schemes 3.1 Anti-lex sus-anchors 3.2 Threshold anchors 3.3 The $t$-gap disappears for large alphabets...| CuriousCoding