Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Maxam-Gilbert Sequencing

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

Lagging Strand Synthesis

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...

Second Uniqueness Theorem

Second Uniqueness Theorem

Consider a region consisting of several individual conductors with a definite charge density in the region between these conductors. The second uniqueness theorem states that if the total charge on each conductor and the charge density in the in-between region are known, then the electric field can be uniquely determined.
In contrast, consider that the electric field is non-unique and apply Gauss's law in divergence form in the region between the conductors and the integral form to the...

Restriction Enzymes

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...

Predicting Products: Substitution vs. Elimination

Predicting Products: Substitution vs. Elimination

When a nucleophile and an alkyl halide react, nucleophilic substitution and β-elimination reactions compete to generate products.
The following factors can influence the mechanisms competing against each other:

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections.

Algorithms for molecular biology : AMB·2020

Same author

Metagenomic analysis through the extended Burrows-Wheeler transform.

BMC bioinformatics·2020

Same author

External memory BWT and LCP computation for sequence collections with applications.

Algorithms for molecular biology : AMB·2019

Same author

Generalized enhanced suffix array construction in external memory.

Algorithms for molecular biology : AMB·2017

Search research articles

Related Experiment Video

Updated: Sep 18, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Faster computation of left-bounded shortest unique substrings.

Larissa L M Aguiar¹, Felipe A Louza²

¹Faculdade de Engenharia Elétrica, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.

Algorithms for Molecular Biology : AMB

|June 20, 2025

Summary

This summary is machine-generated.

This study introduces an efficient algorithm for finding left-bounded shortest unique substrings (LSUS), crucial for applications like PCR primer design. The new method is faster than existing approaches, offering practical speed improvements.

Keywords:

Algorithms Compact data structures Data compression Extraction Grammar

More Related Videos

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Published on: March 12, 2017

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Related Experiment Videos

Last Updated: Sep 18, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Published on: March 12, 2017

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Area of Science:

String processing algorithms
Bioinformatics applications
Computational biology

Background:

Shortest Unique Substrings (SUS) is a key problem in string processing.
Applications include bioinformatics, such as DNA sequence analysis.
A specific variant, Left-Bounded Shortest Unique Substrings (LSUS), is vital for PCR primer design.

Purpose of the Study:

To present a novel, efficient algorithm for the LSUS problem.
To address the need for faster computational methods in bioinformatics.
To provide a practical solution for PCR primer design challenges.

Main Methods:

Developed a linear time O(n) algorithm for LSUS.
Utilized 2n memory words plus n bytes for input strings.
Algorithm designed for efficient string processing.

Main Results:

Achieved O(n) time complexity.
Demonstrated practical speed improvements, averaging two times faster than related methods.
Maintained a comparable peak memory footprint to existing algorithms.

Conclusions:

The presented LSUS algorithm is highly efficient in terms of time complexity.
Offers practical advantages for bioinformatics tasks, especially PCR primer design.
Represents a significant advancement in solving the LSUS problem efficiently.