String Sampling with Bidirectional String Anchors

TL;DR

This paper introduces bidirectional string anchors (bd-anchors), a new string sampling method that improves sample size efficiency and supports fast online pattern searches, addressing limitations of traditional minimizers sampling.

Contribution

The paper proposes bd-anchors, a novel string sampling mechanism with theoretical analysis, practical efficiency, and applications to indexing and pattern search.

Findings

bd-anchors samples decrease proportionally to ll

Sample sizes are competitive or smaller than minimizers

Index construction over bd-anchors is near-linear and space-efficient

Abstract

The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the lexicographically smallest length-$k$ substring in every fragment of $w$ consecutive length-$k$ substrings (in every sliding window of length $w + k - 1$). Minimizers samples are approximately uniform, locally consistent, and computable in linear time. Two main disadvantages of minimizers sampling mechanisms are: first, they do not have good guarantees on the expected size of their samples for every combination of $w$ and $k$; and, second, indexes that are constructed over their samples do not have good worst-case guarantees for on-line pattern searches. We introduce bidirectional string anchors (bd-anchors), a new string sampling mechanism. Given a positive integer $\ell$, our mechanism selects the lexicographically smallest rotation in every length-$\ell$ fragment (in every sliding window of length $\ell$). We show that bd-anchors samples are also approximately uniform, locally consistent, and computable in linear time. In addition, our experiments using several datasets demonstrate that the bd-anchors sample sizes decrease proportionally to $\ell$; and that these sizes are competitive to or smaller than the minimizers sample sizes using the analogous sampling parameters. We provide theoretical justification for these results by analyzing the expected size of bd-anchors samples. As a negative result, we show that computing a total order $\leq$ on the input alphabet, which minimizes the bd-anchors sample size, is NP-hard. We also show that by using any bd-anchors sample, we can construct, in near-linear time, an index which requires linear (extra) space in the size of the sample and answers on-line pattern searches in near-optimal time.