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
Highlights
In sequence analysis the multiple alignment builds the fundament of all proceeding analyses
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 platform independent
Since multiple sequence alignments are the basis of many analyses, for example in phylogenetics or in analysing functional protein domains, there is a need for programs to create and improve those alignments
Summary
In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. 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. Since multiple sequence alignments are the basis of many analyses, for example in phylogenetics or in analysing functional protein domains, there is a need for programs to create and improve those alignments. Editors like JalView [6], SEAVIEW [7], CINEMA [8] or Align [9] are needed to enhance the results by hand. The just mentioned tools are based on sequence information only, but in RNA sequence analyses there is often structural information available.
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