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 commentsTerminology Abstract Preliminaries Methods3.5 Transformations Results Discussion Comments on “Expected density of random minimizers” These are some (biased) comments on “Generating Low-Density Minimizers” (Golan et al. 2024), which introduces the GreedyMini minimizer scheme. At the bottom, there are also some comment on Golan and Shur (2024). Overview The GreedyMinimizer is very cute and simple idea, and works as follows:| Posts on CuriousCoding
Table of Contents 1Sampling schemes1.1Definitions 1.2Miniception 1.3Mod-minimizer 1.4Forward scheme lower bound 1.5Open syncmer minimizer 1.6Open-closed minimizer 1.7New: General mod-minimizer 1.8Variant: Open-closed minimizer using offsets 2Selection schemes2.1Definition 2.2Bd-anchors 2.3New: Smallest unique substring anchors 2.4New: Anti lexicographic sorting 3More sampling schemes3.1Anti-lex sus-anchors 3.2Threshold anchors 3.3The $t$-gap disappears for large alphabets 4Computing the densi...| Posts on CuriousCoding