LibrAlign - A Java library with powerful GUI components for multiple sequence alignment and attached raw and meta data

Stöver BC, Müller KF

Abstract

Several applications currently developed in our group and by cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit these in a graphical user interface. Instead of implementing independent solutions for these different tasks, we decided to develop LibrAlign, a Java library providing reusable and extendable GUI components for MSA data. LibrAlign is fully interoperable with BioJava but its flexible architecture also allows any other storage model for the (alignment) data. A Swing and a SWT version is provided for each component, so LibrAlign can be used in all Java GUI applications, including projects based on the Eclipse Rich Client Platform (RCP) or Bioclipse. The main visual component of LibrAlign (AlignmentArea) displays a MSA and allows efficient manual editing. Additionally, so-called data areas can be attached to each sequence or to the alignment as a whole and display associated data (e.g. trace files, positions of repeat patterns, comments, consensus sequences) directly in the alignment. Custom data areas can easily be created by application developers to deal with new types of data. Among the projects based on LibrAlign currently under development are (i) the Taxonomic Editor of the EDIT platform (which uses the Eclipse RCP), (ii) the alignment editor PhyDE, (iii) AlignmentComparator (which visualizes differences between alternative MSAs of the same dataset), and (iv) HIR-Finder (which locates microstructural mutations like tandem repeats possibly associated with hairpins). Software and poster download: http://bioinfweb.info/LibrAlign

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