SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments
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Summary: Both alignment generation and visualisation 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 visualisation 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. Availability and Implementation: 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.
Copyright 2011 Oxford University Press. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments, Bioinformatics, Volume 28, Issue 7, February, 2012, Pp. 1026-1027 is available online at: http://dx.doi.org/10.1093/bioinformatics/bts035
Structural Biology (incl. Macromolecular Modelling)