4SALE 1.7 is out now


4SALE 1.5 is out now

This release includes a secondary structure viewer, which provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The edit operations were also improved to allow basic sequence modifications.

lara integration

4SALE now integrates lara as a sequence and secondary structure aligment alternative to the 4SALE alignment option. Thanks to Markus Bauer for helping with the integration.

Abstract

Background: In 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.

Results: 4SALE 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.

Conclusions: 4SALE, 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.

If you use this program please cite:

Seibel PN, Müller T, Dandekar T & M Wolf (2008):Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE BMC Research Notes 2008, 1:91. 

Seibel PN, Müller T, Dandekar T, Schultz J & M Wolf (2006): 4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 2006, 7:498.