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dc.contributor.authorWang, Conan K
dc.contributor.authorHofmann, Andreas
dc.date.accessioned2017-07-04T04:41:59Z
dc.date.available2017-07-04T04:41:59Z
dc.date.issued2015
dc.identifier.issn2190-5738
dc.identifier.doi10.1007/s13205-014-0222-0
dc.identifier.urihttp://hdl.handle.net/10072/99078
dc.description.abstractThe mapping of secondary structure elements onto amino acid sequences enhances the quality of alignments frequently used in phylogenetic, genomic and transcriptomic studies, as well as in molecular modelling. Here, we report recent updates to the Java application SBAL, an integrated tool to generate, edit, visualise and analyse secondary structure-based sequence alignments. The main goal of the software is to streamline the work flow in generation of structure-based alignments, and we have thus implemented the option to import and visualise sequence and structure information directly from any PDB file. The new feature is achieved by a Java application named ASSP which follows the original framework of the well-established dictionary of protein secondary structure by Kabsch and Sander. ASSP is also available as a stand-alone application. Other major additions to SBAL include the calculation of distance matrices, peptide properties, as well as detailed on-line tutorials for typical applications.
dc.description.peerreviewedYes
dc.languageEnglish
dc.publisherSpringerOpen
dc.relation.ispartofpagefrom87
dc.relation.ispartofpageto92
dc.relation.ispartofissue1
dc.relation.ispartofjournal3 Biotech
dc.relation.ispartofvolume5
dc.subject.fieldofresearchMedical Parasitology
dc.subject.fieldofresearchBiochemistry and Cell Biology
dc.subject.fieldofresearchcode110803
dc.subject.fieldofresearchcode0601
dc.titleAn integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dcterms.licensehttp://creativecommons.org/licenses/by/4.0/
dc.description.versionVersion of Record (VoR)
gro.rights.copyright© The Author(s) 2014. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
gro.hasfulltextFull Text
gro.griffith.authorHofmann, Andreas
gro.griffith.authorWang, Conan K.


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