Published in Nucleic Acids Res on April 28, 2005
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Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19
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Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (2008) 1.16
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Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics (2009) 1.07
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics (2010) 1.07
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Efficient alignment of RNA secondary structures using sparse dynamic programming. BMC Bioinformatics (2013) 0.95
Robust computational analysis of rRNA hypervariable tag datasets. PLoS One (2010) 0.93
Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res (2008) 0.89
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules. BMC Bioinformatics (2007) 0.89
GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics (2012) 0.88
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput Biol (2014) 0.88
RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA (2012) 0.88
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics (2008) 0.87
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Mind the gaps: progress in progressive alignment. Proc Natl Acad Sci U S A (2005) 0.82
Progressive multiple sequence alignments from triplets. BMC Bioinformatics (2007) 0.82
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Conservation and losses of non-coding RNAs in avian genomes. PLoS One (2015) 0.82
Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics (2010) 0.81
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinformatics (2015) 0.81
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Identifying and searching for conserved RNA localisation signals. Methods Mol Biol (2011) 0.81
Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction? BMC Bioinformatics (2007) 0.80
A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res (2014) 0.80
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics (2011) 0.79
Multi-scale RNA comparison based on RNA triple vector curve representation. BMC Bioinformatics (2012) 0.78
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinformatics (2014) 0.78
Quantifying variances in comparative RNA secondary structure prediction. BMC Bioinformatics (2013) 0.78
Web-Beagle: a web server for the alignment of RNA secondary structures. Nucleic Acids Res (2015) 0.77
NoFold: RNA structure clustering without folding or alignment. RNA (2014) 0.77
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. Bioinformatics (2015) 0.77
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. BMC Bioinformatics (2015) 0.77
Bioinformatics of prokaryotic RNAs. RNA Biol (2014) 0.77
Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res (2008) 0.77
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA. J Theor Biol (2012) 0.77
Evolutionary triplet models of structured RNA. PLoS Comput Biol (2009) 0.77
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences. Nucleic Acids Res (2008) 0.76
Assessing the applicability of the GTR nucleotide substitution model through simulations. Evol Bioinform Online (2007) 0.76
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2011) 0.75
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach. BMC Bioinformatics (2014) 0.75
CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking. PLoS One (2016) 0.75
The complete mitochondrial genome sequence of the little egret (Egretta garzetta). Genet Mol Biol (2015) 0.75
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. Nucleic Acids Res (2014) 0.75
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. Curr Protoc Bioinformatics (2016) 0.75
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation. BMC Bioinformatics (2017) 0.75
Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution. J Mol Evol (2017) 0.75
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Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res (2003) 4.41
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Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol (2002) 3.88
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol (2011) 28.61
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Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res (2011) 1.91
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
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New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res (2011) 1.32
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Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21
Computational RNomics of drosophilids. BMC Genomics (2007) 1.15
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Making automated multiple alignments of very large numbers of protein sequences. Bioinformatics (2013) 1.11
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. PLoS One (2013) 1.09
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res (2008) 1.07
BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res (2011) 0.98
Protein prenyltransferases: anchor size, pseudogenes and parasites. Biol Chem (2003) 0.92
Fast embedding methods for clustering tens of thousands of sequences. Comput Biol Chem (2008) 0.87
Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem (2010) 0.87
High DNA melting temperature predicts transcription start site location in human and mouse. Nucleic Acids Res (2009) 0.83
Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. J Gen Virol (2015) 0.82
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biol (2014) 0.82
Next-generation whole genome sequencing of dengue virus. Methods Mol Biol (2014) 0.80