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

Cluster Sampling Method

Cluster Sampling Method

Appropriate sampling methods ensure that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest.
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...

Wilcoxon Signed-Ranks Test for Matched Pairs

Wilcoxon Signed-Ranks Test for Matched Pairs

The Wilcoxon signed-rank test for matched pairs evaluates the null hypothesis by combining the ranks of differences with their signs. It essentially tests whether the median of the differences in a population of matched pairs is zero. Since the test incorporates more information than the sign test, it generally yields more trustable conclusions. This test also does not require the data to follow a normal distribution, but two conditions must be met for it to be applicable: (1) the data must...

Random Sampling Method

Random Sampling Method

Sampling is a technique to select a portion (or subset) of the larger population and study that portion (the sample) to gain information about the population. Data are the result of sampling from a population. The sampling method ensures that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest. Among the various sampling methods used by...

Sampling Theorem

Sampling Theorem

In signal processing, the analysis of continuous-time signals, denoted as x(t), often involves sampling techniques to convert these signals into discrete-time signals. This process is essential for digital representation and manipulation. A critical component in sampling is the train of impulses, characterized by the sampling interval and the sampling frequency. The relationship between these parameters and the original signal's properties dictates the success of the sampling process.

Sign Test for Matched Pairs

Sign Test for Matched Pairs

The sign test for matched pairs offers a robust method for comparing two paired samples, often for the effects of an intervention in one of them. This method is very useful in situations where the underlying distribution of the data is unknown. The test compares two related samples—often pre- and post-treatment measurements on the same subjects—to determine if there are significant differences in their median values.
To conduct the sign test, we first calculate the differences in...

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

Images in Vascular Medicine: When coronary anatomy goes the wrong way-A diagnostic challenge.

Vascular medicine (London, England)·2026

Same author

Educational Applications of AI-Based Chatbots in Nursing: A Scoping Review.

Nursing reports (Pavia, Italy)·2026

Same author

The Burden of Pediatric Pain: Triggers, Impact on Daily Life and Health Care Utilization-A Cohort Study.

Clinical pediatrics·2026

Same author

The Federated European Genome-Phenome Archive as a global network for sharing human genomics data.

Nature genetics·2025

Same author

Nursing Process for institutionalized older adults: contributions from knowledge awareness workshop.

Revista brasileira de enfermagem·2024

Same author

C1-C2 Transarticular Anterior Fixation for the Treatment of Atlantoaxial Traumatic Dislocation: A Clinical Case.

Revista brasileira de ortopedia·2024

Search research articles

Related Experiment Video

Updated: May 4, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array.

Francisco Fernandes¹, Ana T Freitas

¹Knowledge Discovery and Bioinformatics Group (KDBIO), Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento (INESC-ID), Rua Alves Redol, 9, 1000-029 Lisbon and Department of Computer Science and Engineering, Instituto Superior Técnico (IST) - Universidade de Lisboa, Avenida Rovisco Pais, 1, 1049-001 Lisbon, Portugal.

Bioinformatics (Oxford, England)

|December 17, 2013

Summary

This study introduces a novel, space-efficient method for finding maximal exact matches (MEMs) in large genomic sequences. The new slaMEM software offers a fast and computationally effective approach for bioinformatics analysis.

More Related Videos

Primer-Free Aptamer Selection Using A Random DNA Library

Primer-Free Aptamer Selection Using A Random DNA Library

Published on: July 26, 2010

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Related Experiment Videos

Last Updated: May 4, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

Primer-Free Aptamer Selection Using A Random DNA Library

Primer-Free Aptamer Selection Using A Random DNA Library

Published on: July 26, 2010

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Maximal exact matches (MEMs) are crucial for sequence alignment and string matching.
Existing MEM algorithms use compressed indexes but face computational costs.
High-throughput sequencing generates vast data, necessitating efficient MEM retrieval methods.

Purpose of the Study:

To develop a novel, space-efficient representation for longest common prefix arrays.
To optimize MEM retrieval for FM-Index backward search.
To create a fast and memory-efficient tool for large-scale genomic data analysis.

Main Methods:

Developed a new longest common prefix array-sampled representation.
Optimized the representation for FM-Index backward search.
Implemented the approach in the slaMEM software.

Main Results:

The new representation achieves both speed and space efficiency.
The slaMEM software demonstrates competitive performance against state-of-the-art methods.
Successfully applied the method to efficiently retrieve MEMs from large genomic datasets.

Conclusions:

The developed method offers a significant improvement for MEM retrieval in bioinformatics.
The slaMEM software provides a viable solution for analyzing large genomic datasets.
This approach addresses the challenges posed by the increasing volume of sequencing data.