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

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 syn...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Philipp N. Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf
• Keywords: Associated Secondary Structures, BMCBI 2006, Rna Sequence, Secondary Structure