title: SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  conan.wang@griffith.edu.au
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Structural Chemistry Program, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Qld 4111, Australia. conan.wang@griffith.edu.au
authors.forename: Conan K
authors.initials: CK
authors.lastname: Wang
authors.forename: Ursula
authors.initials: U
authors.lastname: Broder
authors.forename: Saroja K
authors.initials: SK
authors.lastname: Weeratunga
authors.forename: Robin B
authors.initials: RB
authors.lastname: Gasser
authors.forename: Alex
authors.initials: A
authors.lastname: Loukas
authors.forename: Andreas
authors.initials: A
authors.lastname: Hofmann
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D017433:Protein Structure, Secondary; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface