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Created on: 26-Oct-2012   Last updated on: 26-Oct-2012  |  How to cite this?
Total resources - 52
A list of resources for DNA/RNA structures
Akhilesh Bajpai and Sravanthi Davuluri (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
Curves+
http://gbio-pbil.ibcp.fr/Curves_plus
A program for analyzing nucleic acid structures
1
barriers
http://rna.tbi.univie.ac.at/cgi-bin/barriers.cgi
A web-server that provides insights into the folding kinetics of a RNA molecule
42
DIAL™ - DIhedral ALignment Server
http://bioinformatics.bc.edu/clotelab/DIAL
A server to access dynamic programming algorithm for structural alignment of RNA
48
Infernal - INFERence of RNA Alignment
http://infernal.janelia.org
A platform to search DNA sequence databases for RNA structure and sequence similarities
50
LNCipedia.org - A comprehensive compendium of long non-coding RNAs
http://www.lncipedia.org
An integrated database of human annotated long non-coding RNA transcripts, including additional information such as structures and miRNA binding sites
62
ARTS - Alignment of RNA Tertiary Structures
http://bioinfo3d.cs.tau.ac.il/ARTS
A software for alignment of RNA tertiary structures
74
CRW - Comparative RNA Web
http://www.rna.icmb.utexas.edu
A comprehensive resource for RNA structures, families, function, alignments, evolution and comparative analysis
88
ITS2 - Internal Transcribed Spacer 2 Ribosomal RNA Database
http://its2.bioapps.biozentrum.uni-wuerzburg.de
A resource specific to internal transcribed spacer 2 ribosomal RNA
88
NDB - Nucleic Acid Database
http://ndbserver.rutgers.edu
A resource for structural information about nucleic acids
88
RMDB - The RNA Mapping Database
http://rmdb.stanford.edu
A resource for RNA structural mapping data
88
3DNA
http://x3dna.org
A suite for the analysis and visualization of three-dimensional nucleic acid structures, including complicated RNA structures and DNA-protein complexes
92
Cn3D - see in 3D
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
An application that allows to view three-dimensional structures
92
KineFold - RNA/DNA folding predictions including pseudoknots and entangled helices
http://kinefold.curie.fr
A tool for predicting RNA/DNA folding
92
HD-RNAS - Hierarchical Database of RNA Structures
http://www.saha.ac.in/biop/www/HD-RNAS
A resource for functional RNA structures
96
BPS - Database of RNA Base-pair Structures
http://bps.rutgers.edu/bps
A resource for RNA base pairs and related information on the spatial arrangements of interacting bases
97
RAG - RNA AS GRAPHS
http://www.biomath.nyu.edu/rag/home
A resource to classify and analyze RNAs base don topological characteristics
98
3DNALandscapes
http://dcp.rutgers.edu
A resource for exploring the conformational features of DNA
100
CARNA
http://rna.informatik.uni-freiburg.de/CARNA/
A software for multiple alignment of RNA molecules
100
Carnac - RNA structure inference
http://bioinfo.lifl.fr/carnac
A software for predicting secondary structure for a set of homologous RNA sequences
100
ExpaRNA
http://rna.informatik.uni-freiburg.de/ExpaRNA/
A fast and motif-based comparison, and alignment tool for RNA molecules
100
FASTR3D - A Fast and Accurate Search Tool for RNA 3D Structures
http://genome.cs.nthu.edu.tw/FASTR3D
A search tool for RNA three-dimensional structures
100
GISSD - Group I Intron Sequence and Structure Database
http://www.rna.whu.edu.cn/gissd
A specialized database of group I introns' sequence and structure
100
GPRM - Genetic Programming of RNA Motifs
http://bioinfo.cis.nctu.edu.tw/service/gprm
A tool to identify common secondary structure elements within a set of homologous/functionally related RNA sequences
100
URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016)
INFORNA
http://rna.informatik.uni-freiburg.de/INFORNA/
A software to design RNA sequences that fold into a given pseudo-knot free RNA secondary structure
100
LocARNA
http://rna.informatik.uni-freiburg.de:8080/LocARNA/Input.jsp
A software for multiple alignment of RNA molecules
100
MARNA
http://rna.informatik.uni-freiburg.de/MARNA/
A software to compute multiple sequence-structure alignments
100
non-B DB - A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs
http://nonb.abcc.ncifcrf.gov
A resource for predicted non-B DNA-forming motifs in mammalian genomes
100
paRNAss - Prediction of Alternating RNA Secondary Structures
http://bibiserv.techfak.uni-bielefeld.de/parnass
A tool for predicting alternating RNA secondary structures
100
Website recommends the use of their recent tool-RNAshapes as paRNAss is currently out of service (as on 17 Jan 2014)
pknotsRG
http://bibiserv.techfak.uni-bielefeld.de/pknotsrg
A tool for folding RNA secondary structures, including pseudoknots
100
Website recommends the use of latest version of pKiss in place of pknotsRG as the online services of pknotsRG will be discontinued soon.
RNA CoSSMos - Characterization of Secondary Structure Motifs
http://cossmos.slu.edu
A tool for characterization and quantitative analysis of RNA three-dimensional structures
100
RNA FRABASE - RNA FRAgments search engine and dataBASE
http://rnafrabase.ibch.poznan.pl
A resource for RNA sequences and secondary structures
100
RNA STRAND - The RNA secondary STRucture and statistical ANalysis Database
http://www.rnasoft.ca/strand
A resource for known RNA secondary structures of multiple organism
100
RNAalifold
http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi
A software to predict consensus secondary structure from a set of aligned sequences
100
RNABase
http://www.rnabase.org
An annotated database of RNA three-dimensional structures
100
URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016)
RNAbor - Compute structural neighbors of an RNA secondary structure
http://bioinformatics.bc.edu/clotelab/RNAbor
A tool for computing structural neighbors of an RNA secondary structure
100
RNAcofold
http://rna.tbi.univie.ac.at/cgi-bin/RNAcofold.cgi
A tool for predicting secondary structures of single stranded RNA or DNA sequences upon dimer formation
100
RNACompress - Grammar-based compression and informational complexity measurement of RNA secondary structure
http://www.wigs.zju.edu.cn/education/students/liuqi/RNACompress.html
A tool for compression of RNA secondary structure and evaluation of its informational complexity
100
RNAfold
http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
A platform to predict secondary structures of single stranded RNA or DNA sequences
100
RNAinverse
http://rna.tbi.univie.ac.at/cgi-bin/RNAinverse.cgi
A resource that searches for sequences folding into a predefined structure
100
RNAJunction - A database of RNA junction and kissing loop structures
http://rnajunction.abcc.ncifcrf.gov
A resource three-dimensional RNA junction and kissing loop structures with detailed annotations
100
A tool for creating graphical representations of the patterns in an aligned RNA sequences with a consensus structure
100
RNALOSS - Web server for RNA locally optimal secondary structure computation
http://clavius.bc.edu/~clotelab/RNALOSS
A web-server that provides information about the distribution of locally optimal secondary structures
100
RNAMovies
http://bibiserv.techfak.uni-bielefeld.de/rnamovies
A resource for visualization of RNA secondary structure spaces
100
RNAMute - RNA Secondary Structure Mutation Analysis Tool
http://www.cs.bgu.ac.il/~RNAMute
An application for analyzing the effects of point mutations on RNAs secondary structures
100
RNAshapes
http://bibiserv.techfak.uni-bielefeld.de/rnashapes
A tool of RNA structure analysis
100
RNAz
http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi
A tool to detect stable and evolutionarily conserved RNA secondary structures
100
Rsmatch - aligning RNA secondary structures and finding RNA motifs
http://exon.umdnj.edu/Rsmatch
A tool for the alignment of RNA secondary structures, and finding RNA motifs
100
URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016)
SCOR - Structural Classification of RNA
http://scor.berkeley.edu
A comprehensive resource for RNA motif structure, function, tertiary interactions and their relationships
100
Structure Conservation Analysis
http://rna.tbi.univie.ac.at/cgi-bin/SCA.cgi
A tool to detect evolutionarily conserved RNA secondary structures
100
Subviral RNA Database
http://subviral.med.uottawa.ca
A integrated resource and toolbox for viroids and satellite RNAs research
100
The RNA modification database
http://rna-mdb.cas.albany.edu/RNAmods
A comprehensive database for post-transcriptionally modified nucleosides from RNA
100
Vienna RNA Package - RNA Secondary Structure Prediction and Comparison
http://www.tbi.univie.ac.at/~ivo/RNA
A software package for RNA secondary structure prediction and comparison
100
copyright © Dr. Kshitish Acharya K; all rights reserved

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