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

6.6K
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...
6.6K
Sanger Sequencing01:57

Sanger Sequencing

768.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
768.1K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.5K
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...
4.5K
Next-generation Sequencing03:00

Next-generation Sequencing

96.2K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
96.2K
DNA Microarrays02:34

DNA Microarrays

19.8K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
19.8K
Complementary DNA01:44

Complementary DNA

30.6K
Overview
30.6K

You might also read

Related Articles

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

Sort by
Same author

Correction to: Exploring effectiveness of two common trap designs for capturing fish diversity in small freshwater bodies.

Environmental monitoring and assessment·2026
Same author

Exploring effectiveness of two common trap designs for capturing fish diversity in small freshwater bodies.

Environmental monitoring and assessment·2026
Same author

Lactuchelins represent lipopeptide siderophores produced by Pseudomonas lactucae that inhibit Xanthomonas campestris.

The ISME journal·2026
Same author

Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish its interaction with the Ser/Thr kinase CK1α.

Open biology·2026
Same author

Corrigendum to "Long-lines for research monitoring and efficient population regulation of an invasive apex predator, European catfish (<i>Silurus glanis</i>)" [Heliyon Volume 10, Issue 14, 30 July 2024, Article e34125].

Heliyon·2025
Same author

Disruption of the mRNA m6A writer complex triggers autoimmunity in Arabidopsis.

PLoS genetics·2025

Related Experiment Video

Updated: Nov 26, 2025

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
13:49

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

11.7K

Alignment of Biological Sequences with Jalview.

James B Procter1, G Mungo Carstairs2, Ben Soares2

  • 1University of Dundee, Dundee, Scotland, UK. j.procter@dundee.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|December 8, 2020
PubMed
Summary

This chapter details the Jalview platform for creating, analyzing, and publishing multiple sequence alignments. It covers data import, reliability scores, and command-line use for functional site analysis and web publication.

Keywords:
Desktop applicationFunctional site inferenceInteractive analysisMultiple sequence alignment visualizationWeb applicationWeb services

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.8K
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

3.8K

Related Experiment Videos

Last Updated: Nov 26, 2025

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
13:49

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

11.7K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.8K
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

3.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is fundamental for understanding protein and nucleic acid sequence relationships.
  • Jalview is a widely used interactive platform for visualizing and analyzing sequence alignments.
  • Effective MSA creation and analysis are crucial for functional site identification and evolutionary studies.

Purpose of the Study:

  • To introduce the core functionalities of the Jalview platform for MSA.
  • To describe a comprehensive workflow from data import to figure generation using Jalview.
  • To guide users on advanced applications including functional site analysis and web publication of alignments.

Main Methods:

  • Utilizing Jalview's interactive interface for MSA creation and manipulation.
  • Importing alignment reliability scores from external tools like T-Coffee.
  • Employing Jalview's command-line interface for automated analysis and batch processing.
  • Generating publication-quality figures directly from alignment data.

Main Results:

  • Demonstration of a streamlined workflow for MSA creation and analysis in Jalview.
  • Successful integration of T-Coffee reliability scores to assess alignment quality.
  • Capability to perform functional site analysis and identify conserved regions.
  • Facilitation of direct web publication of alignments and associated figures.

Conclusions:

  • Jalview provides a robust and versatile platform for all aspects of multiple sequence alignment.
  • The described workflow enhances efficiency and accuracy in MSA analysis.
  • Jalview empowers researchers to conduct in-depth functional site analysis and share findings effectively online.