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The Jalview Java alignment editor.

Michele Clamp¹, James Cuff, Stephen M Searle

¹The Wellcome Trust Sanger Institute, Hinxton, UK. michele@sanger.ac.uk

Bioinformatics (Oxford, England)

|February 13, 2004

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Manual editing improves automatic multiple sequence alignments. Jalview is a Java tool for efficient viewing and editing of large sequence alignments, aiding in understanding nucleic acid and protein functions.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignment (MSA) is fundamental for analyzing related nucleic acid and protein sequences.
Automatic MSA tools often require manual refinement for optimal accuracy.
Increasing sequence database sizes pose challenges for efficient alignment visualization and editing.

Purpose of the Study:

To introduce Jalview, a Java-based alignment editor.
To provide a tool for efficient visualization and manual editing of large MSAs.

Main Methods:

Development of the Jalview Java application.
Implementation of features for rapid display and manipulation of large sequence alignments.

Main Results:

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Jalview enables fast viewing and editing of extensive multiple sequence alignments.
The tool facilitates improved manual curation of automatically generated alignments.

Conclusions:

Jalview addresses the need for efficient tools in handling large-scale sequence alignment data.
The software supports enhanced analysis of biological sequence function through improved alignment editing.