ArticleBMC bioinformatics2008
ConStruct: Improved construction of RNA consensus structures.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 40 citations in OpenAlex.
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- Modelling the three-dimensional structure of the right-terminal domain of pospiviroids.Scientific reports · 2017Article
- Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS).Archives of virology · 2014Article
- Tackling structures of long noncoding RNAs.International journal of molecular sciences · 2013Review
- Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways.BMC evolutionary biology · 2011Article
- Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions.Nucleic acids research · 2010Article
- Fine-tuning structural RNA alignments in the twilight zone.BMC bioinformatics · 2010Article
- Visualization of multiple alignments, phylogenies and gene family evolution.Nature methods · 2010Review
- Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships.Journal of virology · 2009Review
- Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIA.Genome research · 2009Article
- Informatic resources for identifying and annotating structural RNA motifs.Molecular biotechnology · 2009Review
- RNAalifold: improved consensus structure prediction for RNA alignments.BMC bioinformatics · 2008Article
- Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.BMC research notes · 2008Article
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.