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

Conan K. Wang | Zendy; Ursula Broder | Zendy; Saroja Weeratunga | Zendy; Robin B. Gasser | Zendy; Alex Loukas | Zendy; Andreas Hofmann | Zendy

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

Author(s) -

Conan K. Wang,

Ursula Broder,

Saroja Weeratunga,

Robin B. Gasser,

Alex Loukas,

Andreas Hofmann

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts035

Subject(s) - computer science , visualization , software , java , sequence (biology) , sequence alignment , interface (matter) , data mining , data structure , programming language , peptide sequence , operating system , biochemistry , chemistry , bubble , maximum bubble pressure method , biology , gene , genetics

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.

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