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data structures

Succinct de Bruijn Graphs

This post will give a brief explanation of a Succinct implementation for storing de Bruijn graphs [http://en.wikipedia.org/wiki/De_Bruijn_graph], which is recent (and continuing) work I have been doing with Sadakane. Using our new structure, we have squeezed a graph for a human genome (which

FM-Indexes and Backwards Search

Last time (way back in June! I have got to start blogging consistently again) I discussed a gorgeous data structure called the Wavelet Tree [https://alexbowe.com/wavelet-trees/]. When a Wavelet Tree is stored using RRR sequences, it can answer rank and select operations in $\mathcal{O}(\log{A})$ time,

Wavelet Trees: an Introduction

Today I will talk about an elegant way of answering rank queries on sequences over larger alphabets – a structure called the Wavelet Tree. In my last post [https://alexbowe.com/yarrr-me-hearties] I introduced a data structure called RRR, which is used to quickly answer rank queries on binary sequences, and

RRR: A Succinct Rank/Select Index for Bit Vectors

This blog post will give an overview of a static bitsequence data structure known as RRR, which answers arbitrary length rank queries in $\mathcal{O}(1)$ time, and provides implicit compression. As my blog is informal, I give an introduction to this structure from a birds eye view. If you