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Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

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Accelerating String Comparison in RLZ Compressed Sequences via LCE Jumps.

Rahul Varki, Christina Boucher

Biorxiv : the Preprint Server for Biology

|June 29, 2026

Summary

This summary is machine-generated.

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This study introduces an algorithmic framework for sorting sequences of Relative Lempel-Ziv (RLZ) factors, enhancing compressed data construction. RLZ sorting achieved significant speedups, advancing its use as a foundation for efficient data representation.

Area of Science:

Computer Science
Data Compression
Algorithms

Background:

Relative Lempel-Ziv (RLZ) is effective for compressing large, repetitive data.
Existing methods lack efficient primitives for compressed construction.
RLZ is primarily an archival format, not a tractable representation.

Purpose of the Study:

To develop an algorithmic framework for comparing and sorting RLZ factors.
To enable efficient compressed construction using RLZ.
To advance RLZ from an archival format to a workable representation.

Main Methods:

Introduced a framework for structural comparison and lexicographical sorting of RLZ factor sequences.
Characterized conditions for direct factor comparisons and RLZ-specific shortcuts.

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Published on: June 25, 2014

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

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Last Updated: Jun 30, 2026

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Published on: June 25, 2014

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Developed a method for extending truncated factors to right-maximal matches.

Main Results:

RLZ sorting demonstrated speedups of up to 3.93x compared to character-based sorting.
The framework enables recovery of matching statistics from RLZ parses.
Established efficient primitives for compressed construction using RLZ.

Conclusions:

The proposed framework enhances the utility of RLZ for compressed data construction.
RLZ sorting provides significant performance improvements over traditional methods.
This work lays the foundation for using RLZ as a basis for advanced compressed data structures.