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CARNAC -- Folding Families of Related RNAs
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| To predict conserved secondary structure elements of a family of homologous non-coding RNAs.
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DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
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| Perform the pairwise alignment of two RNA 3D structures.
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Database for mobile group II introns
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| Search for comprehensive information about group II introns. |
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Database of Ribosomal Crosslinks
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| Search for ribosomal cross-linking data.
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FlexStem -- improving predictions of RNA secondary structures with pseudoknots by reducing the search space
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| Predict RNA secondary structures with pseudoknots.
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GPRM -- a genetic programming approach to finding common RNA secondary structure elements
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| Find common secondary structure elements in a set of unaligned coregulated or homologous RNA sequences.
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HyPaLib -- A database of RNAs and RNA structural elements defined by hybrid patterns
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| Search for annotated structural elements characteristic for certain classes of structural and/or functional RNAs.
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ILM -- A Web Server for Predicting RNA Secondary Structures with Pseudoknots
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| Predict RNA secondary structures with pseudoknots.
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INFO-RNA -- A Server for Inverse Folding of RNA
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| Design RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
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IRESite -- The database of experimentally verified IRES structures
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| Search for information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. |
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Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
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| Perform stochastic folding simulations of nucleic acids.
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MeRNA -- a database of metal ion binding sites in RNA structures
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| Search for metal binding sites identified in RNA 3D structures available from the PDB and Nucleic Acid Database.
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Mfold web server for nucleic acid folding and hybridization prediction
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| Predict the secondary structure of RNA and DNA, mainly by using thermodynamic methods. |
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MoD Tools -- regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
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| Discover regulatory motifs in DNA sequences from co-regulated or homologous genes. |
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NCIR -- Non-Canonical Interactions in RNA
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| Search for information on non-canonical base-base interactions in RNA.
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NOBAI -- Numeration of Objects in Biology: Alignment Inferences
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| A web server for character coding of geometrical and statistical features in RNA structure.
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NPInter -- the noncoding RNAs and protein related biomacromolecules interaction database
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| Search for information on functional interactions between noncoding RNAs and proteins in model organisms E. coli, yeast, worm, fly, mouse and human.
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OligoCalc -- An online oligonucleotide properties calculator
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| Calculate DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intra-molecular hairpin loop formation. |
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PARTS -- probabilistic alignment for RNA joinT secondary structure prediction
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| Joint prediction of alignment and common secondary structures of two RNA sequences.
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Pfold -- RNA secondary structure prediction using stochastic context-free grammars
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| Predict a common RNA secondary structure for a given set of RNA sequences.
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ProfDistS -- (Profile-) Distance based phylogeny on sequence - structure alignments
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| A tool for the construction of large phylogenetic trees based on profile distances.
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PseudoViewer -- web application and web service for visualizing RNA pseudoknots and secondary structures
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| Visualize any types of RNA pseudoknots and secondary structures.
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QGRS Mapper -- a web-based server for predicting G-quadruplexes in nucleotide sequences
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| Predict G-quadruplexes in DNA, RNA and oligo sequences. |
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Quadfinder -- server for identification and analysis of quadruplex-forming motifs in nucleotide sequences
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| Identify and analyze quadruplex-forming nucleotide sequences. |
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RADAR -- RNA Data Analysis and Research
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| A web server for RNA data analysis and research.
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RDfolder -- A Web Server for Prediction of RNA Secondary Structure
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| Predict RNA secondary structure using two different methods.
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RNA FRABASE -- database to search three-dimensional fragments within 3D RNA structures
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| Search for 3D RNA fragments within a set of RNA structures.
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RNA Movies -- sequential animation of RNA secondary structures
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| A system for the visualization of RNA secondary structure spaces.
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RNA-related tools on the Bielefeld Bioinformatics Server
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| Use different tools for the analysis of RNA secondary structure.
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RNABase -- An annotated database of RNA structure
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| Search for annotated RNA structural information.
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RNACompress -- compress RNA sequences and their secondary structures
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| Grammar-based compression and informational complexity measurement of RNA secondary structure.
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RNAJunction -- a database of RNA junctions and kissing loops
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| Contains structure and sequence information for RNA structural elements.
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RNALOSS -- a web server for RNA locally optimal secondary structures
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| Analyze RNA secondary structures.
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RNALogo -- a new approach to display structural RNA alignment
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| Create a graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure.
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RNAMST -- efficient and flexible approach for identifying RNA structural homologs
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| Search for RNA structural homologs.
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RNAMute -- RNA Secondary Structure Mutation Analysis Tool
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| An application that provides a user friendly interface for analyzing the effects of point mutations on RNAs secondary structure.
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RNAbor -- a web server for RNA structural neighbors
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| Compute structural neighbors of an RNA secondary structure.
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RNAsoft -- a suite of RNA secondary structure prediction and design software tools
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| Predict the secondary structure of a pair of DNA or RNA molecules.
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RNAz -- prediction of thermodynamically stable and evolutionarily conserved RNA structures
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| Detect thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments.
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RSRE -- RNA structural robustness evaluator
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| Quantitatively evaluate the structural robustness of RNA.
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RegRNA -- an integrated web server for identifying regulatory RNA motifs and elements
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| Identify both sequence and structure homologs of Regulatory RNA motifs and elements. |
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Riboswitch Finder -- A Tool for Identification of Riboswitch RNAs
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| Identify RNA riboswitches.
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SCOR -- Structural Classification of RNA (v.2.0)
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| Search for information on structural classification of RNA.
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SRPDB -- Signal Recognition Particle Database
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| Search for information on sequences, structures and functions of the signal recognition particle.
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The ARTS web server for aligning RNA tertiary structures
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| Conduct structural comparison of RNAs and detect common substructures.
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The European ribosomal RNA database
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| Search for comprehensive information on SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences, structures, taxonomy, and literature. |
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The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
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| Compare and align two RNA sequences.
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The RNA Modification Database
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| Search for information on post-transcriptionally modified nucleosides from RNA.
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The tmRNA website -- reductive evolution of tmRNA in plastids and other endosymbionts
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| To search for sequences, alignments, secondary structures and other information on tmRNA.
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Vienna RNA Websuite
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| A comprehensive collection of tools for folding, design and analysis of RNA sequences.
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WAR -- Webserver for Aligning structural RNAs
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| This server utilizes several tools simultaneously to align and predict the common secondary structure of multiple RNA sequences.
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fRNAdb -- databases to support mining and annotation of functional RNAs
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| Search for information on non-annotated/unannotated non-coding mRNA transcripts. |
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pknotsRG -- tool for folding RNA secondary structures
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| RNA pseudoknot folding including near-optimal structures and sliding windows.
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taveRNA -- a web suite for RNA algorithms and applications
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| Web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA.
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tmRDB -- A tmRNA database
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| Search for aligned, annotated and phylogenetically ordered sequences related to structure and function of tmRNA. |
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