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Updated: Nov 26, 2025
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
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.
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.
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