AlignmentComparator - A GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments

Stöver BC, Müller KF

Abstract

With a growing number of alternative algorithms for automated multiple sequence alignment (MSA) and different strategies for manual alignment corrections it becomes more and more relevant to visualize the differences between alternative MSAs of the same data set. This allows the researcher to decide which alternative alignments to take into account as the bases of e.g. a phylogenetic study or numerous other tasks in biological research. Furthermore, manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm, which both is very relevant in our current research focusing on the improvement of MSA for phylogenetic purposes. Here we present AlignmentComparator, a platform independent open-source GUI application that reveals the differences and shifts in alternative MSAs by calculating and displaying a super alignment (similar to a profile-profile-alignment) that distinguishes between gaps previously contained in a single MSA and super gaps that originated from the comparison. This super alignment allows to directly identify matching regions in the alternative alignments, which otherwise would be very time-consuming with a conventional alignment editor, especially with an increasing column count and therefore a potentially increasing column shift. All differences can be commented and annotated with the AlignmentComparator GUI and saved to a XML file. Software and poster download: http://bioinfweb.info/AlignmentComparator