GraphClust 0.7.6 – Structural Clustering of local RNA Secondary Structures

GraphClust 0.7.6

:: 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

  GraphClust

:: 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

MSARi – Detecting Conservation of RNA Secondary Structure

MSARi

:: 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

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MSARi

:: 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.

LGSFAligner 01 – Align two RNA Secondary Structures Locally

LGSFAligner 01

:: DESCRIPTION

LGSFAligner (Local Gapped Subforest Aligner) is a tool to Align two RNA Secondary Structures Locally

::DEVELOPER

LGSFAligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 LGSFAligner

:: 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.

RNASampler 1.3 – Predict RNA Secondary Structure Motifs

RNASampler 1.3

:: 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

RNASampler

:: 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.

CentroidFold 0.0.16 – Predict RNA Secondary Structure from RNA Sequence

CentroidFold 0.0.16

:: 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

 CentroidFold

:: 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

RNAvista – Prediction of RNA Secondary Structure with Non-canonical Base Pairs

RNAvista

:: 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

  • Web browser

:: 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

zqFold – Predicting RNA Secondary Structure

zqFold

:: DESCRIPTION

zqFold is a simple software for predicting RNA secondary structure. The most development from RNAstructure is that it can predict based on species. For example, if you choose ‘tRNA’, and the sequence will be folded as a cloverleaf; if you choose ‘siRNA’ or ‘microRNA precursor’, it will be folded as a hairpin.

::DEVELOPER

Dr. Quan Zou , Tuo Zhao ,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 zqFold

:: MORE INFORMATION

Citation

Quan Zou, Tuo Zhao, Yang Liu, Maozu Guo.
Predicting RNA secondary structure based on the class information and Hopfield network.
Computers in Biology and Medicine. 2009,39(3):206-214

RNAtips – Analysis of Temperature-induced Changes of RNA Secondary Structure

RNAtips

:: DESCRIPTION

The name RNAtips stands for “temperature-induced perturbation of structure”. The server can be used to analyze the location of temperature-induced changes in the secondary structure of RNA and to compare such changes between two sequences of the same length. This analysis is done by identifying nucleotide regions with a high density of significantly changing positions (clusters).

::DEVELOPER

Department of Genome Oriented Bioinformatics, Technische Universität München

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W486-91. doi: 10.1093/nar/gkt486. Epub 2013 Jun 12.
RNAtips: Analysis of temperature-induced changes of RNA secondary structure.
Chursov A1, Kopetzky SJ, Bocharov G, Frishman D, Shneider A.

McQFold – Predicting RNA Secondary Structures with Pseudoknots by MCMC Sampling

McQFold

:: DESCRIPTION

McQFold is a program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.

::DEVELOPER

Dirk Metzler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C++ Compiler

:: DOWNLOAD

 McQFold

:: MORE INFORMATION

Citation

J Math Biol. 2008 Jan;56(1-2):161-81. Epub 2007 Jun 23.
Predicting RNA secondary structures with pseudoknots by MCMC sampling.
Metzler D, Nebel ME.

ddbRNA – RNA Secondary Structure Prediction

ddbRNA

:: DESCRIPTION

ddbRNA is a software for detection of conserved secondary structures in multiple alignments.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 ddbRNA

:: 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.