CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

Predictions of RNA secondary structure by combining homologous sequence information

(2009) Michiaki Hamada et al.   BIOINFORMATICS

CENTROIDFOLD: a web server for RNA secondary structure prediction

(2009) K. Sato et al.   NUCLEIC ACIDS RESEARCH

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Specific alignment of structured RNA: stochastic grammars and sequence annealing

(2008) Robert K. Bradley et al.   BIOINFORMATICS

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

(2008) C. B. Do et al.   BIOINFORMATICS

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

A fast structural multiple alignment method for long RNA sequences

(2008) Yasuo Tabei et al.   BMC BIOINFORMATICS

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

(2008) Arif Ozgun Harmanci et al.   NUCLEIC ACIDS RESEARCH

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

R-Coffee: a web server for accurately aligning noncoding RNA sequences

(2008) S. Moretti et al.   NUCLEIC ACIDS RESEARCH

Centroid estimation in discrete high-dimensional spaces with applications in biology

(2008) L. E. Carvalho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Measuring Global Credibility with Application to Local Sequence Alignment

(2008) Bobbie-Jo M. Webb-Robertson et al.   PLoS Computational Biology

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH