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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)

S.NoResources
Short description*Rank by usage frequency Click to Edit / Add comments
1Curves+
http://gbio-pbil.ibcp.fr/Curves_plus
A program for analyzing nucleic acid structures
1
2barriers
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
3DIAL™ - DIhedral ALignment Server
http://bioinformatics.bc.edu/clotelab/DIAL
A server to access dynamic programming algorithm for structural alignment of RNA
48
4Infernal - INFERence of RNA Alignment
http://infernal.janelia.org
A platform to search DNA sequence databases for RNA structure and sequence similarities
50
5LNCipedia.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
6ARTS - Alignment of RNA Tertiary Structures
http://bioinfo3d.cs.tau.ac.il/ARTS
A software for alignment of RNA tertiary structures
74
7ITS2 - 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
8RMDB - The RNA Mapping Database
http://rmdb.stanford.edu
A resource for RNA structural mapping data
88
9CRW - Comparative RNA Web
http://www.rna.icmb.utexas.edu
A comprehensive resource for RNA structures, families, function, alignments, evolution and comparative analysis
88
10NDB - Nucleic Acid Database
http://ndbserver.rutgers.edu
A resource for structural information about nucleic acids
88
11Cn3D - see in 3D
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
An application that allows to view three-dimensional structures
92
12KineFold - RNA/DNA folding predictions including pseudoknots and entangled helices
http://kinefold.curie.fr
A tool for predicting RNA/DNA folding
92
133DNA
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
14HD-RNAS - Hierarchical Database of RNA Structures
http://www.saha.ac.in/biop/www/HD-RNAS
A resource for functional RNA structures
96
15BPS - 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
16RAG - RNA AS GRAPHS
http://www.biomath.nyu.edu/rag/home
A resource to classify and analyze RNAs base don topological characteristics
98
17
A tool for creating graphical representations of the patterns in an aligned RNA sequences with a consensus structure
100
18RNALOSS - 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
19RNAJunction - 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
20RNAshapes
http://bibiserv.techfak.uni-bielefeld.de/rnashapes
A tool of RNA structure analysis
100
21RNAinverse
http://rna.tbi.univie.ac.at/cgi-bin/RNAinverse.cgi
A resource that searches for sequences folding into a predefined structure
100
22RNAfold
http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
A platform to predict secondary structures of single stranded RNA or DNA sequences
100
23RNACompress - 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
24RNAcofold
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
25RNAMovies
http://bibiserv.techfak.uni-bielefeld.de/rnamovies
A resource for visualization of RNA secondary structure spaces
100
26RNAMute - 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
27pknotsRG
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.
28RNAz
http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi
A tool to detect stable and evolutionarily conserved RNA secondary structures
100
29Rsmatch - 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)
30SCOR - Structural Classification of RNA
http://scor.berkeley.edu
A comprehensive resource for RNA motif structure, function, tertiary interactions and their relationships
100
31Structure Conservation Analysis
http://rna.tbi.univie.ac.at/cgi-bin/SCA.cgi
A tool to detect evolutionarily conserved RNA secondary structures
100
32Subviral RNA Database
http://subviral.med.uottawa.ca
A integrated resource and toolbox for viroids and satellite RNAs research
100
33The RNA modification database
http://rna-mdb.cas.albany.edu/RNAmods
A comprehensive database for post-transcriptionally modified nucleosides from RNA
100
34Vienna 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
35LocARNA
http://rna.informatik.uni-freiburg.de:8080/LocARNA/Input.jsp
A software for multiple alignment of RNA molecules
100
363DNALandscapes
http://dcp.rutgers.edu
A resource for exploring the conformational features of DNA
100
37CARNA
http://rna.informatik.uni-freiburg.de/CARNA/
A software for multiple alignment of RNA molecules
100
38Carnac - RNA structure inference
http://bioinfo.lifl.fr/carnac
A software for predicting secondary structure for a set of homologous RNA sequences
100
39ExpaRNA
http://rna.informatik.uni-freiburg.de/ExpaRNA/
A fast and motif-based comparison, and alignment tool for RNA molecules
100
40FASTR3D - 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
41GISSD - 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
42GPRM - 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)
43INFORNA
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
44RNAbor - 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
45MARNA
http://rna.informatik.uni-freiburg.de/MARNA/
A software to compute multiple sequence-structure alignments
100
46non-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
47paRNAss - 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)
48RNA CoSSMos - Characterization of Secondary Structure Motifs
http://cossmos.slu.edu
A tool for characterization and quantitative analysis of RNA three-dimensional structures
100
49RNA FRABASE - RNA FRAgments search engine and dataBASE
http://rnafrabase.ibch.poznan.pl
A resource for RNA sequences and secondary structures
100
50RNA 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
51RNAalifold
http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi
A software to predict consensus secondary structure from a set of aligned sequences
100
52RNABase
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)
copyright © Dr. Kshitish Acharya K; all rights reserved

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