BRAliBase: Links to RNA analysis tools.



RNA sequence analysis tools:

Single sequence structure prediction
Single sequence folding
-without pseudoknots
-with pseudoknots
-suboptimal predictions
Comparative structure prediction
Sequence alignment folding
-without pseudoknots
-with pseudoknots
Folding without alignment
-without pseudoknots
-with pseudoknots
Structure alignment
-without pseudoknots
Homology search, data-bases, etc
RNA homology search/gene-finding
-probabilistic: SCFG/CM/HMM
-RNA descriptor/pattern scans
-family specific searches: tRNA/snoRNA/rRNA/miRNA
-miRNA targets
-general (conserved/MFE) structure scans
Alignment Tools
-sequence alignment
-alignment editing tools
-alignment update tools
ncRNA Databases
-sequence alignments + secondary structures
-X-ray and NMR structures
ncRNA phylogenetics
-trees from ncRNA (including structure)
-trees from sequences
Plotting structures
3D tools
Miscellaneous


a program for detecting conservation of RNA secondary structure. It searches orthologous nucleotide sequences for statistically signficant variations conserving a candidate secondary structure.

Single sequence RNA folding algorithms:

Without Pseudoknots

RNAfold*

RNA structure prediction program which ships with the Vienna package. Also a web interface.

Mfold*

Mike Zuker's famous MFE RNA structure prediction algorithm. A more direct link here.

Sfold*

Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities.
RDfolder

RNA folding by energy weighted Monte Carlo simulation.

Afold

Analysis of internal loops within the RNA secondary structure in almost quadratic time

vsfold4

Vsfold4 folds single RNA sequences using an extended energy model.
RNAstructure

A Windows implementation of the Zuker algorithm for RNA secondary structure prediction based on free energy minimization. Includes a sequence editor, an integrated drawing tool, the OligoWalk program, OligoScreen, Dynalign, and a partition function.

CONTRAfold

a novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. By incorporating most of the features found in typical thermodynamic models, CONTRAfold achieves the highest single sequence prediction accuracies to date, outperforming currently available probabilistic and physics-based techniques.

Kinfold

Simulates the stochastic folding kinetics of RNA sequences into secondary structures. The algorithm operates on the basis of the formation, dissociation, and the shifting of individual base pairs.

RNA Kinetics

models the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. The result of the modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend on time. This approach gives comprehensive probabilistic description of RNA folding pathways, revealing important kinetic details that are not captured by the traditional structure prediction methods.

With Pseudoknots

Warning: these gobble computer resources

Pknots-SE

A dynamic programming algorithm for "optimal" RNA pseudoknot prediction.

NUPACK

A dynamic programming algorithm based on the partition function for the prediction of a restricted class of RNA pseudoknots. Uses less resources than Pknots-SE.

Pknots-RG

A dynamic programming algorithm for the prediction of a restricted class of RNA pseudoknots. Uses the least resources to date, conversely infers the most restrictive class of knotted structures.

KineFold

Folding kinetics of RNA sequences including pseudoknots.

HotKnots

A heuristic algorithm for the prediction of RNA secondary structures including pseudoknots.

HPknotter

A Heuristic Approach for Detecting RNA H-type Pseudoknots.

Suboptimal structure prediction

RNAsubopt

Reads RNA sequences from stdin and calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe).

Barriers

Reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier.

Mfold*

Mike Zuker's famous MFE RNA structure prediction algorithm.

Sfold*

Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities.

RNAshapes

Unique suboptimal structures (shapes) are selected based on an abstract representation of RNA secondary structure which is inspired by the dot bracket representation known from the Vienna RNA package. The user can choose from 5 different types of shape resolution corresponding to different abstraction levels.

RNALOSS

locally optimal secondary structure computation. RNALOSS computes the number of k-locally optimal secondary structures for the input RNA, along with relative density of states and minimum free energy of a sample k-locally optimal secondary structure.

RNA folding with alignment (Plan A):

Without Pseudoknots

Pfold*

Folds alignments using a SCFG trained on rRNA alignments. The alignment length limit is 500.

RNAalifold*

Folds alignments using a combination of free-energy and a covariation measure. Ships with the Vienna package. Also a web-server.

RNA-Decoder and CORSmodel

Programmes for comparative predictions of RNA secondary structure in regions which are also protein coding.

ConStruct V2.0

A tool for thermodynamic controlled prediction of conserved secondary structure. Also allows iterative manual alignment refinement.

Genebee

RNA alignment folding using a combination of free-energy and mutual information.

RNAGA

Prediction of common secondary structures of RNAs by genetic algorithm.

GArna

Prediction of secondary structures of RNAs by genetic algorithm.

GPRM

finding common secondary structure elements, not a global alignment, in a sufficiently large family (e.g. more than 15 members) of unaligned RNA sequences.

X2s

An X windows program for analyzing and editing an alignment of RNA sequences and for predicting RNA secondary structure. The original server (http://tyrant.ucsc.edu/X2s/) appears to be dead. Files provided c/o A. Wilm.

BayesFold

Finds, ranks, and draws the likeliest structures for a sequence alignment. Foldings are based on the predictions of the Bayesian statistical method. Your browser must be Internet Explorer 5+ for Windows with the Adobe Scalable Vector Graphics Viewer plugin installed! - I don't have either.

With Pseudoknots

KNetFold

Computes a consensus RNA secondary structure from an RNA sequence alignment based on machine learning.

ILM*

Iterated Loop Matching. Evaluates stems in an alignment using a combination of free-energy and mutual information. Iteratively selects high scoring stems.

HXMATCH

Hxmatch computes the consensus structure including pseudoknots based on an alignment of a few RNA sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm.

MIfold

Matlab package for investigating mutual information content of RNA alignments.

Circles

Circles is an experimental Windows 95/98/NT program for inferring RNA secondary structure using the comparative method. It provides a user-friendly interface to Jack Tabaska's maximum weight matching programs. The user can read in an alignment in FASTA, Clustal, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in standard formats.

RNA folding without alignment (Plan B):

Without Pseudoknots

T-LARA

Produce a global fold and alignment of ncRNA families using integer linear programming and Langrangian relaxation.

Consan

Pairwise RNA structural alignment, both unconstrained and constrained on alignment pins. Consans uses a constrained version of a pairSCFG structural alignment algorithm which assumes knowledge of a few confidently aligned positions (pins). Pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment.

CMfinder

An RNA motif prediction tool. It is an expectation maximization algorithm using covariance models for motif description, carefully crafted heuristics for effective motif search, and a novel Bayesian framework for structure prediction combining folding energy and sequence covariation. This tool performs well on unaligned sequences with long extraneous flanking regions, and in cases when the motif is only present in a subset of sequences. CMfinder also integrates directly with genome-scale homology search, and can be used for automatic refinement and expansion of RNA families.

caRNAc*

Computer Alignment of RNA by Cofolding. VERY fast and VERY selective.

PMmatch

A variant of the Sankoff algorithm from the Vienna group.

Stemloc

Comparative RNA structure-finder using accelerated pairwise stochastic context-free grammars. Ships with the 'dart' package by Ian Holmes.

Dynalign*

Uses a "full energy model" and comparative information to align and fold 2 sequences. Restricts the 'span' of base-pairs to improve CPU time.

Foldalign*

Predicts conserved local sequence and hair-pin structures using CONSENSUS and CLUSTAL-like heuristics. Primarily used to infer cis-regulatory elements.

Foldalign 2

New: Structurally align two sequences using a light weight energy model in combination with RIBOSUM like score matrices.

RNAcast

RNA consensus abstract shapes technique: an alternative to the Sankoff algorithm for multiple RNA folding.

scaRNA

Stem Candidate Aligner for RNA: aligns two RNA sequences and calculates similarities, based upon estimated common secondary structures. Scarna is a fast, convenient tool for clustering RNA sequences and for similarity search in long sequences. It works even for pseudoknotted secondary structures. Currently www.scarna.org Only works with Internet Explorer!

COVE

COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis.

Slash

A combination of COVE and Foldalign.

SEED

Suffix arrays are used enumerate complementary regions, possibly containing interior loops, as well for matching RNA secondary structure expressions..

With Pseudoknots

comRNA

comRNA predicts common RNA secondary structure motifs in a group of related sequences. The current implementation (July 2004) returns an ambigious structure notation.

RNA structure alignment (Plan C):

Without Pseudoknots

RNAforester*

Compare and align RNA secondary structures via a "forest alignment" approach.

MARNA*

MARNA considers both primary sequence and the secondary structure to align RNAs. Based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases.

MiGaL

Compare RNA secondary structures and build phylogenetic trees.

LGSFAligner

A tool to align two RNA secondary structures locally.

RNA_align

Aligns two RNA structures using an edit distance model.

RAGA

RNA Alignment by Genetic Algorithm: RAGA is a pairwise alignment program. Its aim is to align two RNA sequences, sharing the same secondary structure but different primary sequences, knowing the secondary structure of one of the RNAs. It sounds like this approach has more in common with Infernal than with bonafide "Plan C" methods.

With Pseudoknots

PSTAG

Pair stochastic tree adjoining grammars (PSTAGs) for aligning and predicting RNA secondary structures including a simple type of pseudoknots which can represent most of known pseudoknot structures.

RNA homology search/gene-finding:

Probabilistic: SCFG/CM/HMM

Infernal

Construct a profile based upon an alignment and consensus structure, this can be used to scan a database and append sequences to the alignment. The Rfam database is maintained using Infernal.

RSEARCH

RSEARCH aligns an RNA query to target sequences, using SCFG algorithms to score both secondary structure and primary sequence alignment simultaneously. It's slow, but somewhat more capable of finding significant remote RNA structure homologies than sequence alignment methods like BLAST.

RSmatch

RNA Secondary Structure Matcher: provides four functions: (1) regular database search, (2) multiple structure alignment, (3) iterative database search, and (4) pairwise sequence alignment.

COVE

COVE is an implementation of stochastic context free grammar methods for RNA sequence/structure analysis. As far as I can tell this has largely been replaced by Infernal.

ERPIN

ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developed by Daniel Gautheret and André Lambert

RaveNnA

A software package for faster covariance models whilst provably sacrificing no accuracy for rigorous filtering. Also includes heuristic filters.

PHMMTS

An implementation of the "pair hidden Markov models on tree structures (PHMMTSs)".

HomoStRscan

A program for discovering homologous RNAs in complete genomes by taking a single RNA sequence with its secondary structure.

RNACAD

A stochastic context-free grammar(SCFG) RNA modeling package that accounts for both primary and secondary structure information. SCFGs are robust and allow arbitrary deviations from a pattern.

RNA descriptor/pattern scans

MilPaT

Motifs and Inter-moLecular motifs searching tool using Constraints Solving Problems formAlism and solving Technique.

GUUGle

A utility for fast exact matching under RNA base pairing rules. GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.

RNAMST

an efficient and flexible RNA Motif Search Tool for RNA structural homologs. RNAMST web server accepts four different kinds of input formats to facilitate user to describe a RNA structure easily.

RNAMotif

Construct descriptors based upon consensus models of structural RNAs, these can be used to scan data-bases for matches.

RNAbob

RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules.

HyPa

A system for the declarative description and efficient search of hybrid patterns in large genomic data sets.

PatScan

PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.

Family specific searches

tRNAscan-SE

tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.

snoscan

This program and its use to find 2'-O-methylation guide (C/D box) snoRNAs has been described in Lowe & Eddy, "A Computational Screen for Methylation Guide snoRNAs In Yeast", Science 283: 1168-1171, 1999.

snoGPS Server

Search for pseudo-uridylation guide (H/ACA box) snoRNA genes in a genomic sequence at the "Lowe Lab". One can also download and locally install the published version of from the supplementary materials.

MiRscan

Search for pre-miRNA molecules in genomic sequences.

BRUCE

A program for the detection of transfer-messenger RNA genes in nucleotide sequences

ARAGORN

A program to detect tRNA genes and tmRNA genes in nucleotide sequences.

SRPscan

Prediction of SRP RNA genes in genomic DNA sequences

CITRON

Automatic identification of group I intron cores in genomic DNA sequences.

RNAlign

Takes a sequence for the third domain of the insect mitochondrial small subunit (12S) rRNA gene and aligns it with an existing databank. The server returns an alignment and secondary structure model for your sequence.

miRNA targets

RNAhybrid

a tool for finding the minimum free energy hybridisation of a long and a short RNA. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

RNAcofold

Calculate secondary structures of two RNAs with dimerization.

RNAduplex

Compute the structure upon hybridization of two RNA strands.

UNAfold

Prediction of hybridization and melting for double-stranded nucleic acids.

miRanda

an algorithm for finding genomic targets for microRNAs

TargetRNA

Predict mRNA targets of basepairing sRNAs using stacking energies and P-value calculation using extreme-value distributions.

DIANA-MicroT Analyzer

A tool for prediction of MicroRNA targets using free energy.

PicTar

PicTar is an algorithm for the identification of microRNA targets.

General structure search

RNAz

RNAz is program for predicting structurally conserved and thermodynamic stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.

Alifoldz

Assessing a multiple sequence alignment for the existence of an unusual stable and conserved RNA secondary structure.

EvoFold

A comparative method for identifying functional RNA structures in multiple-sequence alignments. It is based on a probabilistic model-construction called a phylo-SCFG and exploits the characteristic differences of the substitution process in stem-pairing and unpaired regions to make its predictions. Each prediction consists of a specific secondary structure and a folding potential score.

QRNA

This is the code from Elena Rivas that accompanies a submitted manuscript "Noncoding RNA gene detection using camparative sequence analysis". QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures.

MSARi

RANDfold

Assess the stability of non-coding RNA secondary structures such as micro RNAs, transfer RNAs and ribosomal RNAs compared to random sequences.

MSARi

A program for detecting conservation of RNA secondary structure. It searches orthologous nucleotide sequences for statistically signficant variations conserving a candidate secondary structure.

RNAGenie

A computational approach to identify genes for functional RNAs in genomic sequences

NCRNASCAN

This is the code from Elena Rivas that goes with the paper "Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs" by Elena Rivas and Sean Eddy. As the title indicates, the genefinder doesn't work, because real RNAs don't generally have any more secondary structure content than random sequence, contrary to what we expected.

RNAProfile

An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Input a set of unaligned RNA sequences expected to share a common motif, RNAProfile outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules.

HMMGCC

Noncoding RNA genes identified in AT-rich hyperthermophiles

RNAAnalyzer

you can search your RNA/DNA for several known RNA structures and retrieve some general information of your sequence

ddbRNA

detection of conserved secondary structures in multiple alignments

Alignment Tools:

Sequence Alignment

ProbCons

Probabilistic Consistency-based Multiple Alignment of RNA sequences.

ProAlign

A probabilistic multiple alignment program. Our recommended method for sequence-based structured RNA alignment!

MAFFT

MAFFT ver.5.6 - Multiple alignment program for amino acid or nucleotide sequences. The updated versions of MAFFT now performs very well on our benchmark data.

MUSCLE

Public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for multiple sequence comparison by log-expectation. Recent (since 21/05/05) updates to MUSCLE (v3.52) code have resulted in improvements of this algorithm on ncRNA data since our published benchmark.

Clustal

A multiple sequence alignment program. Clustal, despite its great age (or maybe because of), is also superior to many alternative alignment tools (for structured RNA alignment).

POA

Multiple sequence alignment using partial order graphs. Produces (comparatively) reasonable sequence-based alignments in an extremely short amount of time! Recommended if speed is an issue. NB. Using both the global and progressive modes is recommended.

prrn

Global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method.

Editing

RALEE

RALEE is a major mode for the Emacs text editor. It provides functionality to aid the viewing and editing of multiple sequence alignments of structured RNAs.

jPHYDIT

jPHYDIT displays secondary/tertiary structure pairings of ribosomal RNA molecules whilst users edit nucleotide sequences. This produces "alignments based on RNA secondary structure" required for the precise phylogenetic inference and structure analysis.

The ARB project

A graphically oriented package comprising various tools for sequence database handling and data analysis.

DCSE

DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system and checking of incorporated RNA structure.

SeaView

SeaView is a graphical multiple sequence alignment editor, runs on *nix, Mac, Windows,...

Belvu

Belvu is an X-windows viewer for multiple sequence alignments.

Updating

RNA db tools

a collection of tools which can be used to perform semi-automated update of RNA structural databases.

Infernal

cmalign aligns the RNA sequences in seqfile to the covariance model (CM) in cmfile, and outputs a multiple sequence alignment.

COVEMF

COVEMF is a modification of Sean Eddy's COVE package implementing stochastic context free grammar (SCFG) methods for RNA sequence/structure analysis. COVEMF 2.4.4 is a superset of COVE version 2.4.4; it provides all programs that COVE provides in the original plus two additional programs, COVEAM and COVEAF - for easily and quickly add sequences to an existing RNA alignment.

ncRNA Databases:

Sequence alignments + secondary structures

Rfam

Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.

Ribosomal Database Project-II

Faster, smarter, stronger: The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated 16S rRNA sequences.

European rRNA database

Compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.

Free energy parameters

The current free energy nearest neighbor parameters from Doug Turner's lab.

CRW Site

Alignments, structure models and phylogenetic analyses of 5S, 16S and 23S rRNA, Group I and II introns and tRNA.

SRPDB

SRPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP.

The tmRNA Website

Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website, a collection of 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, Vienna.

X-ray and NMR structures

NDB

The nucleic acid database: a repository of three-dimensional structural information about nucleic acids

RNABase.org

The RNA Structure Database: consolidates all RNA containing structures from both the NDB and RCSB (formerly PDB). Every entry is automatically checked for conformational errors.

IMB-Jena PDB/NDB RNA structures

This compilation includes all structures that contain at least one O2* atom in the nucleotides G,C,A,T,U or +G,+C,+A,+T,+U.

SCOR

a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships. SCOR 2.0.2 provides a survey of the three-dimensional motifs contained in 497 NMR and X-ray RNA structures available as of May 15, 2003. This includes 5,865 secondary structural elements, of which 2,103 are hairpin loops and 3,762 are internal loops. The structural elements are organized in a directed acyclic graph (DAG) architecture, allowing multiple parent classes for a motif.

ncRNA phylogenetics:

trees from ncRNA

PHASE

Designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. Substitution models of sequence evolution that consider pairs of sites rather than single sites are implemented in this package along with standard nucleotides substitution models used nowadays. When a RNA molecule with a secondary structure is used in conjunction with a RNA substitution model, PHASE requires a structure-based alignment of the sequences with the consensus secondary structure indicated in bracket and dot notation at the top of the alignment.

RRNADIST, RRNAML, RNAML

Empirical substitution models for Ribosomal RNA. Estimate phylogeny using maximum likelihood structural RNA models of sequence evolution.

MrBayes

Bayesian Inference of Phylogeny. Allows doublet (secondary structure) models.

SISSI

Simulating Sequence Evolution with Site-Specific Interactions: a software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices.

jRNA

Exploring insect (and other less interesting) phylogenies using RNA secondary structure. Provides tools structural RNA alignment and analysis.

CBCanalyzer

Inferring phylogenies based on compensatory base changes.

trees from sequences

PHYLIP

A free package of programs for inferring phylogenies. And much more.

Drawing RNA structures:

RNAplot

Draw RNA Secondary Structures. Available formats are: PostScript (ps), Graph Meta Language (gml), Scalage Vector Graphics (svg), and XRNA save file (xrna).

RNAfamily

A simple software tool that enables the display of all secondary structures for a family of RNA molecules. Uses a linear backbone representation.

NAVIEW

A group of programs and scripts that produce plots of RNA secondary structures. Also available here.

RnaViz

A user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules.

XRNA

a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams

RNAdraw

an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows

loopDloop

a tool for drawing RNA secondary structures in molecular biology

SStructView

a Java applet for viewing RNA secondary structures and linking to multiple computational backends

RNAView/RnamlView

generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions

PseudoViewer2

Automatically visualizing RNA pseudoknot structures as planar graphs. Needs Windows .NET Framework for "in web" use, else exe is available....

3D tools:

S2S

Sequence to Structure (S2S) : display, manipulate and interconnect RNA data from the sequence to the structure. A very nice tool integrating 3D, 2D and 1D structure and comparative information.

Ribostral

An RNA 3D alignment analyzer and viewer based on basepair isostericities.

COMPADRES

Find, automatically and without prior knowledge, recurrent RNA motifs in three-dimensional structures.

AMIGOS/PRIMOS/Qnifft

Tools for playing with RNA/DNA pdb files. AMIGOS reads an RNA PDB file and outputs a complete table of torsion angle calculations. PRIMOS allows the user to perform interactive comparisons between RNA structures and to conduct database searches for specific RNA structures or substructures. Qnifft utilizes the non-linear Poisson-Boltzmann (NLPB) equation to calculate the electrostatic potentials of nucleic acids.

Miscellaneous:

RNALfold

computes locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA structures.

RNA Movies

a system for the visualization of RNA secondary structure spaces

paRNAss

Prediction of Alternating RNA Secondary Structures

Riboswitch Finder

search your RNA/DNA for several known Riboswitches

RNAmute

A user friendly interface for analyzing the effects of point mutations on RNAs secondary structure.

RNAmutants

Analysis of mutations in RNA sequences

RandFold

Computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

MatrixPlot

Mutual information in RNA and DNA sequences.

RNA Structure Logo

The structure logo is an extension of the sequence logo by Schneider and Stephens. We have extended the standard sequence logo to cope with any prior nucleotide distribution as well as allowing for gaps in the alignments, and indicate mutual information of basepaired positions in RNA.

Tinoco Plot

a simple tool to investigate possible secondary structure elements in RNA or DNA single strands

The RNA World Website

This web resource lists Internet links on RNA related topics.

RNAsoft

Software for RNA/DNA secondary structure prediction and design. PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules. CombFold predicts which strand, out of a combinatorial set formed from DNA or RNA input strands, folds to a secondary structure with the lowest minimum free energy. RNA Designer designs an RNA sequence that folds to a given input secondary structure.


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Paul Gardner, <pg5@sanger.ac.uk>
Dept. of Evolutionary Biology, University of Copenhagen,
Universitetsparken 15, 2100 Copenhagen Ø, Denmark.

Time-stamp: 2005-07-19 10:21:24 pgardner