{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T13:56:57Z","timestamp":1765807017216},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0conan.wang@griffith.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts035","type":"journal-article","created":{"date-parts":[[2012,2,14]],"date-time":"2012-02-14T01:23:09Z","timestamp":1329182589000},"page":"1026-1027","source":"Crossref","is-referenced-by-count":20,"title":["SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments"],"prefix":"10.1093","volume":"28","author":[{"given":"Conan K.","family":"Wang","sequence":"first","affiliation":[{"name":"1 Structural Chemistry Program, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Qld 4111, 2Department of Veterinary Science, The University of Melbourne, Vic 3052, 3James Cook University, Cairns, Qld 4878 and 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