An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements

The mapping of secondary structure elements onto amino acid sequences enhances the quality of alignments frequently used in phylogenetic, genomic and transcriptomic studies, as well as in molecular modelling. Here, we report recent updates to the Java application SBAL, an integrated tool to generate, edit, visualise and analyse secondary structure-based sequence alignments. The main goal of the software is to streamline the work flow in generation of structure-based alignments, and we have thus implemented the option to import and visualise sequence and structure information directly from any PDB file. The new feature is achieved by a Java application named ASSP which follows the original framework of the well-established dictionary of protein secondary structure by Kabsch and Sander. ASSP is also available as a stand-alone application. Other major additions to SBAL include the calculation of distance matrices, peptide properties, as well as detailed on-line tutorials for typical applications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13205-014-0222-0) contains supplementary material, which is available to authorized users.