Jalview Version 2--a multiple sequence alignment editor and analysis workbench

Abstract

Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.

Availability: The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org.

Fig. 1.

Capabilities of the Jalview 2 desktop application. Ovals depict major capabilities: visualization, interactive editing, analysis and WYSIWYG figure generation. Arrows connect bioinformatics data handled by JV2 with flat-file or web-service data sources. Analysis includes built-in alignment conservation and tree building algorithms, and web services for MSA and secondary structure prediction methods. The screenshot of the application shows two sets of sequences for proteins in the lactate dehydrogenase family. One contains an alignment of protein sequences retrieved from the Uniprot database, the other their coding sequences retrieved from the EMBL database. Interactive highlighting shows the region corresponding to the amino acid or codon position near the mouse pointer in both the alignment windows and the Jmol structure display of a PDB record associated with one protein.