1 | Curves+ http://gbio-pbil.ibcp.fr/Curves_plus | A program for analyzing nucleic acid structures |
| | |
2 | 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 |
| | |
3 | DIAL - DIhedral ALignment Server http://bioinformatics.bc.edu/clotelab/DIAL | A server to access dynamic programming algorithm for structural alignment of RNA |
| | |
4 | Infernal - INFERence of RNA Alignment http://infernal.janelia.org | A platform to search DNA sequence databases for RNA structure and sequence similarities |
| | |
5 | 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 |
| | |
6 | ARTS - Alignment of RNA Tertiary Structures http://bioinfo3d.cs.tau.ac.il/ARTS | A software for alignment of RNA tertiary structures |
| | |
7 | CRW - Comparative RNA Web http://www.rna.icmb.utexas.edu | A comprehensive resource for RNA structures, families, function, alignments, evolution and comparative analysis |
| | |
8 | 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 |
| | |
9 | NDB - Nucleic Acid Database http://ndbserver.rutgers.edu | A resource for structural information about nucleic acids |
| | |
10 | RMDB - The RNA Mapping Database http://rmdb.stanford.edu | A resource for RNA structural mapping data |
| | |
11 | 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 |
| | |
12 | Cn3D - see in 3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml | An application that allows to view three-dimensional structures |
| | |
13 | KineFold - RNA/DNA folding predictions including pseudoknots and entangled helices http://kinefold.curie.fr | A tool for predicting RNA/DNA folding |
| | |
14 | HD-RNAS - Hierarchical Database of RNA Structures http://www.saha.ac.in/biop/www/HD-RNAS | A resource for functional RNA structures |
| | |
15 | 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 |
| | |
16 | RAG - RNA AS GRAPHS http://www.biomath.nyu.edu/rag/home | A resource to classify and analyze RNAs base don topological characteristics |
| |
|
17 | 3DNALandscapes http://dcp.rutgers.edu | A resource for exploring the conformational features of DNA |
| | |
18 | CARNA http://rna.informatik.uni-freiburg.de/CARNA/ | A software for multiple alignment of RNA molecules |
| | |
19 | Carnac - RNA structure inference http://bioinfo.lifl.fr/carnac | A software for predicting secondary structure for a set of homologous RNA sequences |
| | |
20 | ExpaRNA http://rna.informatik.uni-freiburg.de/ExpaRNA/ | A fast and motif-based comparison, and alignment tool for RNA molecules |
| | |
21 | 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 |
| | |
22 | 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 |
| | |
23 | 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 |
| | URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016) |
24 | 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 |
| | |
25 | LocARNA http://rna.informatik.uni-freiburg.de:8080/LocARNA/Input.jsp | A software for multiple alignment of RNA molecules |
| | |
26 | MARNA http://rna.informatik.uni-freiburg.de/MARNA/ | A software to compute multiple sequence-structure alignments |
| | |
27 | 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 |
| | |
28 | paRNAss - Prediction of Alternating RNA Secondary Structures http://bibiserv.techfak.uni-bielefeld.de/parnass | A tool for predicting alternating RNA secondary structures |
| | Website recommends the use of their recent tool-RNAshapes as paRNAss is currently out of service (as on 17 Jan 2014) |
29 | pknotsRG http://bibiserv.techfak.uni-bielefeld.de/pknotsrg | A tool for folding RNA secondary structures, including pseudoknots |
| | Website recommends the use of latest version of pKiss in place of pknotsRG as the online services of pknotsRG will be discontinued soon. |
30 | RNA CoSSMos - Characterization of Secondary Structure Motifs http://cossmos.slu.edu | A tool for characterization and quantitative analysis of RNA three-dimensional structures |
| | |
31 | RNA FRABASE - RNA FRAgments search engine and dataBASE http://rnafrabase.ibch.poznan.pl | A resource for RNA sequences and secondary structures |
| | |
32 | 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 |
| | |
33 | RNAalifold http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi | A software to predict consensus secondary structure from a set of aligned sequences |
| | |
34 | RNABase http://www.rnabase.org | An annotated database of RNA three-dimensional structures |
| | URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016) |
35 | 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 |
| | |
36 | 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 |
| | |
37 | 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 |
| | |
38 | RNAfold http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi | A platform to predict secondary structures of single stranded RNA or DNA sequences |
| | |
39 | RNAinverse http://rna.tbi.univie.ac.at/cgi-bin/RNAinverse.cgi | A resource that searches for sequences folding into a predefined structure |
| | |
40 | 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 |
| | |
41 | RNALogo - a new approach to display structural RNA alignment http://rnalogo.mbc.nctu.edu.tw | A tool for creating graphical representations of the patterns in an aligned RNA sequences with a consensus structure |
| | |
42 | 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 |
| | |
43 | RNAMovies http://bibiserv.techfak.uni-bielefeld.de/rnamovies | A resource for visualization of RNA secondary structure spaces |
| | |
44 | 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 |
| | |
45 | RNAshapes http://bibiserv.techfak.uni-bielefeld.de/rnashapes | A tool of RNA structure analysis |
| | |
46 | RNAz http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi | A tool to detect stable and evolutionarily conserved RNA secondary structures |
| | |
47 | 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 |
| | URL not working as on 17 Jan 2014 (confirmed on 3 Nov 2016) |
48 | SCOR - Structural Classification of RNA http://scor.berkeley.edu | A comprehensive resource for RNA motif structure, function, tertiary interactions and their relationships |
| |
|
49 | Structure Conservation Analysis http://rna.tbi.univie.ac.at/cgi-bin/SCA.cgi | A tool to detect evolutionarily conserved RNA secondary structures |
| | |
50 | Subviral RNA Database http://subviral.med.uottawa.ca | A integrated resource and toolbox for viroids and satellite RNAs research |
| | |
51 | The RNA modification database http://rna-mdb.cas.albany.edu/RNAmods | A comprehensive database for post-transcriptionally modified nucleosides from RNA |
| | |
52 | 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 |
| | |