SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments

Bioinformatics
Conan K WangAndreas Hofmann

Abstract

Both alignment generation and visualization are important processes for producing biologically meaningful sequence alignments. Computational tools that combine reliable, automated and semi-automated approaches to produce secondary structure-based alignments with an appropriate visualization of the results are rare. We have developed SBAL, a tool to generate and edit secondary structure-based sequence alignments. It is easy to install and provides a user-friendly interface. Sequence alignments are displayed, with secondary structure assignments mapped to their corresponding regions in the sequence by using a simple colour scheme. The algorithm implemented for automated and semi-automated secondary structure-based alignment calculations shows a comparable performance to existing software. SBAL has been implemented in Java to provide cross-platform compatibility. SBAL is freely available to academic users at http://www.structuralchemistry.org/pcsb/. Users will be asked for their name, institution and email address. A manual can also be downloaded from this site. The software, manual and test sets are also available as supplementary material. conan.wang@griffith.edu.au Supplementary data are available at Bioinformatics online.

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Citations

Aug 16, 2012·BMC Bioinformatics·Saroja WeeratungaAndreas Hofmann
Jun 1, 2013·Parasites & Vectors·Cinzia CantacessiAlex Loukas
Nov 26, 2015·Biotechnology Advances·Namitha MohandasRobin B Gasser
May 16, 2015·Scientific Reports·Bert BreugelmansRobin B Gasser
Oct 12, 2013·Scientific Reports·Cinzia CantacessiAndreas Hofmann
Jul 20, 2014·International Journal for Parasitology·Bert BreugelmansRobin B Gasser
Apr 25, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Megan CrossAndreas Hofmann
Nov 20, 2016·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Megan CrossAndreas Hofmann

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