title: ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach.
abstract: Secondary structures of RNA sequences are increasingly being used as additional information in reconstructing phylogenies and/or in distinguishing species by compensatory base change (CBC) analyses. However, in most cases just one secondary structure is used in manually correcting an automatically generated multiple sequence alignment and/or just one secondary structure is used in guiding a sequence alignment still completely generated by hand. With the advent of databases and tools offering individual RNA secondary structures, here we re-introduce a twelve letter code already implemented in 4SALE - a tool for synchronous sequence and secondary structure alignment and editing - that enables one to align RNA sequences and their individual secondary structures synchronously and fully automatic, while dramatically increasing the phylogenetic information content. We further introduce a scaled down non-GUI version of 4SALE particularly designed for big data analysis, and available at: http://4sale.bioapps.biozentrum.uni-wuerzburg.de.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany. Electronic address: matthias.Wolf@biozentrum.uni-wuerzburg.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Wolf
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Koetschan
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
mesh_terms: D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000737:chemistry / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S
keywords: 4SALE; Alignment; ITS2 database; Phylogeny; ProfDistS