:: DESCRIPTION
ddbRNA is a software for detection of conserved secondary structures in multiple alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2003 Sep 1;19(13):1606-11.
ddbRNA: detection of conserved secondary structures in multiple alignments.
di Bernardo D, Down T, Hubbard T.
:: DESCRIPTION
GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs.
::DEVELOPER
Freiburg Bioinformatics Group.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Steffen Heyne, Fabrizio Costa, Dominic Rose, Rolf Backofen
GraphClust: alignment-free structural clustering of local RNA secondary structures
Bioinformatics, 2012, 28(12), i224-i232
:: DESCRIPTION
The MSARi (Multiple Sequence Alignments for Statistical Detection of RNA Secondary Structure) program indentifies conserved RNA secondary structure in non-coding RNA genes and mRNAs by searching multiple sequence alignments of a large set of candidate catalogs for correlated arrangements of reverse-complementary regions
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. Epub 2004 Aug 10.
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.
Coventry A, Kleitman DJ, Berger B.
:: DESCRIPTION
LGSFAligner (Local Gapped Subforest Aligner) is a tool to Align two RNA Secondary Structures Locally
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J Comput Biol. 2006 Apr;13(3):702-18.
Local gapped subforest alignment and its application in finding RNA structural motifs.
Jansson J, Hieu NT, Sung WK.
:: DESCRIPTION
RNASampler is a program that predicts common RNA secondary structure motifs in a group of related sequences.RNASampler finds the common structures between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures and subsequently recalculates stem conservation using the updated probabilities. The iterative process terminates upon convergence of the sampled structures.
::DEVELOPER
Stormo Lab in Department of Genetics, Washington University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Xing Xu, Yongmei Ji, and Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics, August 2007; 23: 1883 – 1891.
:: DESCRIPTION
CentroidFold predicts an RNA secondary structure from an RNA sequence. FASTA and one-sequence-in-a-line format are accepted for predicting a secondary structure per sequence. It also predicts a consensus secondary structure when a multiple alignment (CLUSTALW format) is given. CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.
::DEVELOPER
Computational Biology Research Center (CBRC),
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kengo Sato, Michiaki Hamda, Kiyoshi Asai, Toutai Mituyama,
CentroidFold: a web application for RNA secondary structure prediction,
Nucl. Acids Res. (2009) 37 (suppl 2): W277-W280
:: DESCRIPTION
RNAvista is a webserver to assess RNA secondary structure with non-canonical base pairs based on user-provided sequence or secondary structure containing canonical base pairs only.
::DEVELOPER
The Bioinformatics Group, Poznan University of Technology.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2019 Jan 1;35(1):152-155. doi: 10.1093/bioinformatics/bty609.
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs.
Antczak M, Zablocki M, Zok T, Rybarczyk A, Blazewicz J, Szachniuk M
:: DESCRIPTION
rnalocopt is a web server that computes the partition function and samples structures from the ensemble of locally optimal secondary structures of a given RNA sequence. Here, a locally optimal secondary structure is one for which the free energy can not be lowered by the addition or removal of a single base pair (i.e. a kinetic trap in unit resolution energetics).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
W.A. Lorenz, P. Clote.
Computing the partition function for kinetically trapped RNA secondary structures.
Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178.
:: DESCRIPTION
RNApathfinder is a web server to compute near-optimal folding pathways between two given secondary structures for a given RNA sequence. Since this problem is known to be NP-complete, our main algorithm, RNAtabupath uses the TABU local search heuristic. The web server includes both downloadable source code for several algorithms, as well as a web engine to compute pathways. Intended applications concern folding pathways for RNA conformational switches.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
I. Dotú, W.A. Lorenz, P. Van Hentenryck, P. Clote.
Computing folding pathways between RNA secondary structures.
Nucleic Acids Res. 2010 Mar 1;38(5):1711-22.
:: DESCRIPTION
RNAborMEA computes the maximum expected accurate δ-neighbors of a given RNA secondary structure for a given RNA sequence. Here, a structure T is a δ-neighbor of a given structure S, if S can be transformed into T by a minimum number δ of edit operations, where an edit operation consists of removing or adding a single base pair (i.e. if the base pair distance between S and T is δ).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Feng Lou and Peter Clote.
Maximum expected accurate structural neighbors of an RNA secondary structure.
Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), Feb 3-5, 2011. Orlando, FL.