Improving the accuracy of predicting secondary structure for aligned RNA sequences

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

(2010) Sayed Mohammad Ebrahim Sahraeian et al.   NUCLEIC ACIDS RESEARCH

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

(2009) M. Hamada et al.   BIOINFORMATICS

Predictions of RNA secondary structure by combining homologous sequence information

(2009) Michiaki Hamada et al.   BIOINFORMATICS

Exact Calculation of Distributions on Integers, with Application to Sequence Alignment

(2009) Lee A. Newberg et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Advances in RNA Structure Prediction from Sequence: New Tools for Generating Hypotheses about Viral RNA Structure-Function Relationships

(2009) S. J. Schroeder   JOURNAL OF VIROLOGY

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

(2009) Roman R. Stocsits et al.   NUCLEIC ACIDS RESEARCH

CENTROIDFOLD: a web server for RNA secondary structure prediction

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

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

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

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

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

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

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

(2008) Christoph Jöchl et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner 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

Measuring Global Credibility with Application to Local Sequence Alignment

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