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  • Title: SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.
    Author: Wang CK, Broder U, Weeratunga SK, Gasser RB, Loukas A, Hofmann A.
    Journal: Bioinformatics; 2012 Apr 01; 28(7):1026-7. PubMed ID: 22332239.
    Abstract:
    SUMMARY: 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. 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. CONTACT: conan.wang@griffith.edu.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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