4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

By Philipp N. Seibel, T. Müller, Thomas Dandekar, Jörg Schultz, M. Wolf. BMC Bioinformatics, 2006

389 citations recorded by the source corpus.

BackgroundIn sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously.Results4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.Conclusion4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1aac76d18fbb74d9b6946bfe2c06aecebc4e5155

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In Molecular Biology

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Citations in the corpus

• Specificity in communities of Symbiodinium in corals from Johnston Atoll (2009, methodology): “…IT2S folding was conducted using previously published Symbiodinium ITS2 structures as templates (Hunter et al. 2007, Thornhill et al. 2007) in the ITS2 database interactive website (Schultz et al. 2006, Selig et al. 2008) and manually edited using the software 4SALE (Seibel et al. 2006, 2008).”
• Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals (2010, positive): “(A) Alignment of the primary sequences of four species from the genus Heterodera of Heteroderidae; (B) Alignment of the primary sequences of four species from four genera of Heteroderidae; and (C) Alignment of the primary sequences of four species from four families of animals aided by secondary str”
• Taxonomic reassessment of the genus Mychonastes (Chlorophyceae, Chlorophyta) including the description of eight new species (2011, methodology): “The ITS-2 sequences were aligned according to secondary structure using 4SALE (Seibel et al. 2006, 2008).”
• A bloom of Karlodinium australe (Gymnodiniales, Dinophyceae) associated with mass mortality of cage-cultured fishes in West Johor Strait, Malaysia (2014, methodology): “The multiple sequence-structure alignment of Karlodinium ITS2 was generated using an ITS sequence structure-specific scoring matrix (Seibel et al., 2006) in 4SALE v.”
• ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus (2010, methodology): “Sequences and secondary structures were automatically aligned with 4SALE 1.5 using an ITS2-specific scoring matrix for sequences and structures (Seibel et al. 2006, 2008).”
• A fast structural multiple alignment method for long RNA sequences (2008, methodology): “developed an alignment tool with an editor, which uses the secondary structure information of individual sequences to align multiple RNA sequences with low time complexities (4SALE) [22].”
• Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species. (2011, methodology): “To locate hemi–compensatory base changes (hemi–CBCs) and CBCs, the ITS–2 secondary structure was constructed with the help of mfold (zuker 2003) and 4SALE (seiBel et al. 2006, 2008).”