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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
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...
4.9K
RNA-seq03:21

RNA-seq

12.6K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.6K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
5.7K
Introduction to R01:11

Introduction to R

5.3K
R is a powerful software environment for statistical computing and graphics. Originating as an implementation of the S language, developed at Bell Laboratories, R has evolved into a robust, open-source statistical software favored by statisticians and data scientists worldwide. Its comprehensive suite includes data manipulation, calculation, and graphical display capabilities, making it versatile for data analysis and visualization. Its programming language is at the core of R's...
5.3K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

7.6K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.6K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.3K
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...
7.3K

You might also read

Related Articles

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

Sort by
Same author

VN-EGNN: E(3)- and SE(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification.

Journal of cheminformatics·2025
Same author

Mean arterial pressure is all you need in a machine learning model for mean arterial pressure prediction.

European journal of anaesthesiology·2025
Same author

Lipid Ratios for Diagnosis and Prognosis of Pulmonary Hypertension.

American journal of respiratory and critical care medicine·2025
Same author

Machine learning prediction of unexpected readmission or death after discharge from intensive care: A retrospective cohort study.

Journal of clinical anesthesia·2024
Same author

In Defense of Metrics: Metrics Sufficiently Encode Typical Human Preferences Regarding Hydrological Model Performance.

Water resources research·2024
Same author

Potential Predictors for Deterioration of Renal Function After Transfusion.

Anesthesia and analgesia·2024
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Apr 4, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

527

msa: an R package for multiple sequence alignment.

Ulrich Bodenhofer1, Enrico Bonatesta1, Christoph Horejš-Kainrath1

  • 1Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.

Bioinformatics (Oxford, England)
|August 29, 2015
PubMed
Summary
This summary is machine-generated.

The new msa R package offers a unified interface for popular multiple sequence alignment tools like ClustalW, ClustalOmega, and MUSCLE. It also integrates with the shade package for customizable visualization of sequence alignments.

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

758
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.4K

Related Experiment Videos

Last Updated: Apr 4, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

527
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

758
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The R platform and Bioconductor packages are prevalent in bioinformatics.
  • Multiple sequence alignment is a fundamental bioinformatics task.
  • Previous R packages have not adequately addressed multiple sequence alignment.

Purpose of the Study:

  • To introduce the msa R package, providing a unified interface for multiple sequence alignment.
  • To integrate popular alignment algorithms within the R environment.
  • To offer flexible visualization capabilities for sequence alignments.

Main Methods:

  • Developed the msa R package, integrating ClustalW, ClustalOmega, and MUSCLE.
  • Ensured the package runs on all major platforms without external software dependencies.
  • Integrated the shade package for enhanced alignment visualization.

Main Results:

  • The msa package provides a novel, unified R interface for multiple sequence alignment.
  • It simplifies the execution of established alignment algorithms within R.
  • Offers customizable plotting of multiple sequence alignments via the shade package.

Conclusions:

  • The msa package addresses a gap in R's bioinformatics toolkit for multiple sequence alignment.
  • It enhances the utility of R for genomic and proteomic data analysis.
  • Facilitates reproducible and visually informative sequence alignment studies.