ConStruct: Improved construction of RNA consensus structures

Background: Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. Results: We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the init...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger
• Keywords: BMCBI 2008, Consensus Structure, Consensus Structure Prediction, Tertiary Interactions