Structural Genomics @CNAG CRG

RNA bioinformatics resources

Name Description
Tertiary structure databases
NDB the nucleic acid database
SCOR a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.
Alignment and consensus secondary structure databases
CRW Site alignments, structure models and phylogenetic analyses of 5S, 16S and 23S rRNA, Group I and II introns and tRNA.
Rfam a large collection of multiple sequence alignments and covariance models covering common non-coding RNA families.
Ribosomal Database Project-II The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community.
RiboWeb RiboWeb is composed of the serveral integrated RNA information resources.
RNA FRABASE RNA FRAgments search engine and dataBASE.
Silva A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.
SRPDB the Signal Recognition Particle Database contains aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP.
The tmRNA Website Research a collection of tmRNA sequences, alignments, secondary structures and other information.
tmRDB tmRDB (tmRNA Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of tmRNA.
The RNase P Database a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information.
Viral RNA Structure Database Viral structures from TBI.
General sequence alignment methods
BLAST The Basic Local Alignment Search Tool (BLAST) compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
CLUSTALW a general purpose multiple sequence alignment program.
FASTA a searcher for local alignments against proteins and nucleotides databases.
MUSCLE MUltiple Sequence Comparison by Log-Expectation.
T-COFFEE a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, protein sequences and structures.
RNA alignment methods by 2D structural information
LGSFAligner a Local Gapped Subforest Aligner for pairs of RNA secondary structures.
LocARNA LocARNA is a tool for multiple alignment of RNA molecules.
MiGaL a program for comparing RNA secondary structures and building phylogenetic trees.
RNA_align aligns two RNA structures using an edit distance model.
RNAdistance a program for calculating measures for secondary structure dissimilarity.
RNAforester a program for comparing and aligning RNA secondary structures via the "forest alignment" approach.
RNAshapes a program that uses the "consensus shapes" method to predict an abstract shape common to RNA sequences.
Alignment methods for RNA 2D structures with pseudoknots
PSTAG a pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures.
RNA searching methods by sequence/structural information
ERPIN an RNA motif search program.
HomoStRscan a program for discovering homologous RNAs in complete genomes.
Infernal a program to construct a RNA profile based upon an alignment and consensus structure.
RADAR a web-based server for RNA data analysis and research.
RaveNnA a software package for fast covariance modeling of RNA sequences.
RNACAD a stochastic context-free grammar (SCFG) RNA modeling package.
RNAmotif a program for searching a database for RNA sequences that match a "motif" of secondary structure interactions.
RSEARCH a program for aligning an RNA query to target sequences, using SCFG algorithms.
Palingol a descriptive programming language to describe nucleic acid's secondary structure and scan sequence databases.
PHMMTS an implementation of pair hidden Markov models on tree structures.
RNA phylogenetic analysis tools
CBCanalyzer a program for inferring phylogenies based on compensatory base changes.
jRNA a program for exploring insect (and other less interesting) phylogenies using RNA secondary structure.
MrBayes a program for the Bayesian estimation of phylogeny.
PHASE a program designed for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA.
RRNADIST, RRNAML and RNAML a program for modeling empirical substitutions for Ribosomal RNA.
SISSI a software tool for generating data of related sequences along a given phylogeny.
RNA folding software
Afold a program for analyzing internal loops within RNA secondary structures.
alteRNA alteRNA is an alternative to many RNA folding methods.
CONTRAfold a secondary structure prediction method based on conditional log-linear models (CLLMs).
inteRNA inteRNA predicts the joint secondary structure of two RNA sequences.
Kinfold a program to simulate the stochastic folding kinetics of RNA sequences into secondary structures.
MC-FOLD/MC-Sym The MC-Fold | MC-Sym pipeline is a web-hosted service for RNA secondary and tertiary structure prediction.
RNAfold an MFE RNA structure prediction algorithm.
RNA Kinetics a program to simulate the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule.
RNAstructure a Windows implementation of the Zuker algorithm for RNA secondary structure prediction based on free energy minimization.
Sfold a statistical sampling of all possible RNA secondary structures.
UnaFold (MFold) an MFE RNA structure prediction algorithm.
Vsfold4 a program that folds single RNA sequences using an extended energy model.
RNA single sequence 2D prediction with pseudoknots
HotKnots a heuristic algorithm for the prediction of RNA secondary structures including pseudoknots.
Hpknotter a heuristic approach for detecting RNA H-type pseudoknots.
KineFold a folding kinetics program of RNA sequences including pseudoknots.
McQFold a program for MCMC-sampling secondary structures with pseudoknots for a given RNA sequence.
NUPACK a dynamic programming algorithm based on the partition function for the prediction of a restricted class of RNA pseudoknots.
Pknots-RG a dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots.
Pknots a dynamic programming algorithm for optimal RNA pseudoknot prediction using the nearest neighbour energy model.
Algorithm for 2D with suboptimal predictions
Barriers a program to compute local minima and energy barriers of the RNA folding landscape.
RNALOSS a program for local and optimal secondary structure computation.
RNAshapes a program to select unique suboptimal structures (shapes) based on an abstract representation of RNA secondary structure.
RNAsubopt a program to calculate all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe).
Algorithm for 2D with suboptimal predictions with pseudoknots
MPGAfold A massively parallel genetic algorithm for predicting RNA secondary structures with pseudoknots.
RNA 2D prediction by alignments
BayesFold a program to find, rank, and draw the likeliest structures for a sequence alignment.
ConStruct a tool for thermodynamic controlled prediction of conserved secondary structure.
Garna a program for predicting secondary structures of RNAs using a genetic algorithm.
Genebee a RNA alignment folding program that uses a combination of free-energy and mutual information.
Pfold a program for folding alignments using a SCFG trained on rRNA alignments.
RNAalifold a program for folding alignments using a combination of free-energy and a co-variation measures.
RNAlishapes a tool for RNA structure analysis based on aligned RNA sequences.
RNAGA a program for predicting common RNA secondary structures using a genetic algorithm.
RNA 2D prediction by alignments with pseudoknots
Circles an experimental Windows 95/98/NT program for inferring RNA secondary structure using a comparative method.
HXMATCH a program for computing a consensus structure including pseudoknots based on an alignment of a few RNA sequences.
ILM an iterated loop matching program that evaluates stems in an alignment using a combination of free-energy and mutual information.
KnetFold a program that computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning approaches.
Mifold a matlab package for investigating mutual information content of RNA alignments.
Simultaneous alignment and structure prediction methods
CaRNAc a program for comparative analysis combined with MFE folding.
Cmfinder an RNA motif prediction tool.
Consan a program to produce pairwise RNA secondary structural alignments.
COVE an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.
Dynalign a "full energy model" and comparative information to align and fold 2 two RNA sequences.
Foldalign a program that predicts conserved local sequence and hair-pin structures using CONSENSUS and CLUSTAL-like heuristics.
LARA a program that produces a global fold and alignment of ncRNA families using integer linear programming and Lagrangian relaxation.
RNAcast a RNA consensus abstract shapes technique for multiple RNA folding.
RNAmine is a software tool for extracting the structural motifs from a set of RNA sequences.
SEED a program that uses suffix arrays to enumerate complementary regions, possibly containing interior loops, as well for matching RNA secondary structure expressions.
Stemloc a comparative RNA-structure finder that uses accelerated pairwise stochastic context-free grammars.
Simultaneous alignment and structure prediction methods with pseudoknots
comRNA a program for predicting common RNA secondary structure motifs in a group of related sequences.
RNA Tertiary structural tools
AMIGOS/PRIMOS/Qnifft a series of tools for working with RNA/DNA structure files.
Assemble a graphical tool to construct and study RNA structures.
ARTS Alignment of RNA Tertiary Structures based on quadrats RNA representation.
BERNACLE a Python library for RNA 3D structure prediction.
ERNA-3D a program to create and manipulate RNA 3D coordinates.
FARNA/FARFAR a program for predicting RNA 3D structure using the Web version of the Rosetta server
FR3D a program for finding small RNA motifs (two to 20 nucleotides) in PDB files
iFoldRNA a web portal for interactive RNA folding simulations.
MC-Sym a software that builds RNA 3-D structures using coordinates and relations between residues extracted from X-ray crystallography and NMR.
MANIP a program that allows the rapid assembly of separate motifs into a complex three-dimensional architecture.
ModeRNA a program for comparative RNA modeling.
NAB a program to construct models for non-helical nucleic acids.
NASSAM a program that searches for motifs and formations of nucleic acid bases in 3D space within nucleic acid PDB formatted structures.
NAST a Nucleic Acid Simulation Tool.
Ribostral an RNA 3D alignment analyzer and viewer based on basepair isostericities.
RNA2D3D a program that can generate, view and compare RNA 3D structures available in the package StructureLab
RNABuilder/MMB a tool for building 3D RNA models using a variety of knowledge the user has about the structure.
RNAComposer a user-friendly program to the fully automated prediction of large RNA 3D structures.
RNA-MolIP an integer programming framework that refines predicted secondary structures.
ROSETTA The Rosetta Commons aims to develop high resolution protein/RNA prediction and design software.
S2S a program to display, manipulate and interconnect RNA sequence and strucure data.
VFold software package to evaluate the stable structures and the folding free energies for RNA secondary structures and pseudoknotted structures.s.
YUP a package for molecular simulations of reduced representation models.
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