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Related Experiment Video

Updated: Apr 25, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

QuickEd: high-performance exact sequence alignment based on bound-and-align.

Max Doblas^1,2, Oscar Lostes-Cazorla^1,3, Quim Aguado-Puig^1,3,4

¹Computer Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.

Bioinformatics (Oxford, England)

|March 13, 2025

Summary

This summary is machine-generated.

QuickEd offers optimal sequence alignment for long reads, overcoming scalability issues with a novel bound-and-align strategy. This method significantly speeds up analysis while maintaining accuracy and low memory usage.

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Published on: June 28, 2018

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Pairwise sequence alignment is crucial for analyzing sequencing data.
Long-read sequencing technologies are increasingly popular but pose scalability challenges for classical algorithms.
Existing heuristic methods often sacrifice accuracy for speed.

Purpose of the Study:

To introduce QuickEd, a novel sequence alignment algorithm designed for long and noisy sequencing data.
To address the scalability limitations of traditional alignment algorithms in the era of long-read sequencing.
To provide an accurate and efficient alignment tool that maintains optimal alignment.

Main Methods:

Developed QuickEd, utilizing a bound-and-align strategy.
Employs heuristic strategies to efficiently bound the maximum alignment score.
Reduces computational complexity from O(n^2) to O(ns^) for optimal alignment.

Main Results:

QuickEd achieves significant speedups compared to state-of-the-art tools like Edlib (4.2-5.9×) and BiWFA (3.8-4.4×).
Maintains optimal alignment accuracy for long and noisy datasets.
Demonstrates a stable memory footprint below 35 MB for sequences up to 1 Mbp.

Conclusions:

QuickEd provides a scalable and accurate solution for long-read sequence alignment.
The bound-and-align strategy effectively balances speed and accuracy.
QuickEd is a valuable tool for modern genomic data analysis.