ConStruct: Improved construction of RNA consensus structures
Open Access
- 28 April 2008
- journal article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 9 (1) , 219
- https://doi.org/10.1186/1471-2105-9-219
Abstract
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.Keywords
This publication has 61 references indexed in Scilit:
- Semiautomated improvement of RNA alignmentsRNA, 2007
- SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC FrameworkPLoS Computational Biology, 2007
- Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?BMC Bioinformatics, 2007
- Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based ClusteringPLoS Computational Biology, 2007
- Query-Dependent Banding (QDB) for Faster RNA Similarity SearchesPLoS Computational Biology, 2007
- Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNAGenome Research, 2006
- Structural Basis for Ribosome Recruitment and Manipulation by a Viral IRES RNAScience, 2006
- MAFFT version 5: improvement in accuracy of multiple sequence alignmentNucleic Acids Research, 2005
- Dynalign: an algorithm for finding the secondary structure common to two RNA sequencesJournal of Molecular Biology, 2002
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994