ArticleBMC bioinformatics2006
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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111 citing papers in PubMed.
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- 18S rDNA sequence-structure phylogeny of the eukaryotes simultaneously inferred from sequences and their individual secondary structures.BMC research notes · 2024Article
- Findings on three endocommensal scuticociliates (Protista, Ciliophora) from freshwater mollusks, including their morphology and molecular phylogeny with descriptions of two new species.Marine life science & technology · 2024Article
- Genomic characterisation and ecological distribution ofFrontiers in microbiology · 2024Article
- GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2.BMC plant biology · 2023Article
- Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation inJournal of fungi (Basel, Switzerland) · 2023Article
- Structure-Based GC Investigation Sheds New Light on ITS2 Evolution inInternational journal of molecular sciences · 2023Article
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- Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances.Plants (Basel, Switzerland) · 2022Article
- Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity ofFrontiers in microbiology · 2022Article
- First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora).Frontiers in microbiology · 2022Article
51 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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