LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data
Stöver BC, Müller KF
Abstract in Online-Sammlung (Konferenz)
Zusammenfassung
Several applications currently developed in our group and by our cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit it in a graphical user interface (GUI). Instead of implementing independent solutions for these different tasks, we decided to create a library containing powerful and reusable common GUI components. Since this library is open source (GNU GPL 3) it can be used and extended by other researchers, who are then able to focus on the core functionality of their applications, but can still provide a user-friendly GUI. Besides components allowing the displaying and editing of MSAs, several types of data (e.g. trace files, comments, statistical sequence information, positions of tandem repeats, hairpins or inversions) can be attached either to single sequences or to the alignment as a whole. All these data views implement a common interface that makes it easy for developers to create new custom views. Several components from our library (e.g. displaying different types of data) can be connected to each other in the application they are embedded in, so that the user can scroll through one of them while all others will automatically display the data associated with the current position. LibrAlign is fully interoperable with the BioJava API and all components are provided in a native Swing and a native SWT version (the two major GUI frameworks for Java), so that they can be integrated into any Java GUI application, including projects based on the Eclipse Rich Client Platform or Bioclipse. Several software projects based on LibrAlign are currently in development in- and outside our group. Among those are (i) the Taxonomic Editor of the EDIT platform which is extended to support sequence and alignment associated data for the Campanula portal of EDIT, (ii) a new version of the alignment editor PhyDE, (iii) AlignmentComparator (an application to visualize differences between alternative automatic and manual alignments, which we currently use in study investigating the influence of manual alignment corrections on phylogenetic studies), and (iv) HIR-Finder (an application which locates microstructural mutations like tandem repeats possibly associated with hairpins). LibrAlign download: http://bioinfweb.info/LibrAlign
Details zur Publikation
Veröffentlichungsjahr: 2014
Sprache, in der die Publikation verfasst ist: Englisch
Link zum Volltext: http://ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=93978