Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

13.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
13.5K
Multiple Comparison Tests01:13

Multiple Comparison Tests

4.0K
Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
4.0K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.3K
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...
4.3K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.4K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.4K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.9K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.9K

You might also read

Related Articles

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

Sort by
Same author

Metabologenomic profiling of the endemic Australian fungus <i>Aspergillus luteorubrus</i>.

Mycology·2026
Same author

Structural motif search across the protein universe with Folddisco.

Nature biotechnology·2026
Same author

A novel method to select Reference Proteomes in UniProt.

bioRxiv : the preprint server for biology·2026
Same author

Reference-free discovery with barcoded single-cell sequencing.

Nature biotechnology·2026
Same author

FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning.

bioRxiv : the preprint server for biology·2026
Same author

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.

Nature biotechnology·2026
Same journal

Correction to 'SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome'.

NAR genomics and bioinformatics·2026
Same journal

asms: finding allele-specific methylation in human genomes without phasing.

NAR genomics and bioinformatics·2026
Same journal

An epigenetic clock for chronological age estimation in East Asian populations.

NAR genomics and bioinformatics·2026
Same journal

The role of ATF4 in neurons under mitochondrial stress.

NAR genomics and bioinformatics·2026
Same journal

Distinct repeat architecture landscapes in the proteomes of protozoan parasites.

NAR genomics and bioinformatics·2026
Same journal

Long non-coding RNA triplex-dependent regulation of melanoma gene networks.

NAR genomics and bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Sep 13, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K

An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment

Luisa Santus1,2, Jose Espinosa-Carrasco1, Leon Rauschning1,3

  • 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.

NAR Genomics and Bioinformatics
|August 1, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a new nf-core framework for deploying and evaluating multiple sequence alignment (MSA) tools in high-performance computing (HPC) environments. This framework aims to simplify tool selection and comparison for bioinformatics researchers dealing with complex computational challenges.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Related Experiment Videos

Last Updated: Sep 13, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Bioinformatics problems often require heuristic solutions due to computational complexity, leading to numerous tools with no single best performer.
  • Identifying optimal tools and managing diverse methods is challenging for users and developers, especially with growing data volumes.
  • Standardized frameworks are needed for seamless tool deployment and comparison in high-performance computing (HPC) environments.

Purpose of the Study:

  • To present a pilot nf-core framework for streamlined deployment and rigorous performance evaluation of multiple sequence alignment (MSA) tools.
  • To address the challenges in selecting and comparing heuristic solutions for computationally complex bioinformatics problems.
  • To provide a proof of principle for a broader bioinformatics community beyond MSA.

Main Methods:

  • Development of an nf-core framework tailored for the MSA software ecosystem.
  • Integration of popular multiple sequence alignment tools within the framework.
  • Design for rigorous performance evaluation and comparison of MSA methods.

Main Results:

  • A pilot nf-core framework, nf-core/multiplesequencealign, has been designed and implemented.
  • The framework facilitates streamlined deployment and evaluation of MSA tools.
  • Demonstrates a standardized approach for managing and comparing heuristic bioinformatics software.

Conclusions:

  • The nf-core/multiplesequencealign framework offers a standardized solution for MSA tool deployment and evaluation.
  • This framework serves as a valuable resource for the MSA community and a model for other bioinformatics fields.
  • It addresses the need for efficient management and comparison of heuristic computational methods in bioinformatics.