Abstract
BackgroundAligning 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.ResultsWe 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 initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity.ConclusionCONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and requirements section of this article.
Highlights
Aligning homologous non-coding RNAs correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions
CONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints
The CONSTRUCT package can be downloaded from the URL listed in the Availability and requirements section of this article
Summary
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 are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Structure prediction may provide insight into RNA function, and pattern-based database searches [1,2] may reveal new homologues, without the need for time-consuming experiments. Prerequisite for these predictions and (page number not for citation purposes). Automatically generated alignments often need to be corrected or refined by hand, which is a complex and tedious task To ease this task a few sophisticated RNA alignment editors exist, e. One of these tools is CONSTRUCT (construction of RNA consensus structures; [16]), which is an RNA alignment editor and allows for a variety of consensus structure predictions
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