metaserver
Overview
RNA metaserver is a gateway to RNA folding methods.
It provides two kinds of services:
First, predicting the secondary structure given an RNA sequences. For that, eleven different methods are ran either locally or on remote servers. The MetaRNA server collects the results, and displays them all at once.
Second, aligning multiple RNA sequences based on their secondary structures. The nine methods for that included in MetaRNA subdivide into methods for simultaneous alignment and structure prediction (Sankoff-like methods), and pure alignment methods. All have in common that they read a set of RNA sequences, and return a multiple alignment. The resulting alignments are collected and displayed.
Methods for secondary structure prediction
| Method | Description | Reference | URL |
|---|---|---|---|
| Afold | Analysis of internal loops within the RNA secondary structure in almost quadratic time [local] | Ogurtsov et al. 2006 | ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold |
| RNAfold | RNA structure prediction program that comes with the Vienna package [local] | Hofacker 2004 | http://www.tbi.univie.ac.at/RNA |
| PknotsRG | 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 [local] | Reeder et al. 2007 | http://bibiserv.techfak.uni-bielefeld.de/pknotsrg |
| Pknots | A dynamic programming algorithm for "optimal" RNA pseudoknot prediction. [local] | Rivas & Eddy 1999 | http://selab.janelia.org/software.html |
| Contrafold | A 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. [local] | Do et al. 2006 | http://contra.stanford.edu/contrafold |
| McQfold | MCMC-sampling secondary structures with pseudoknots for a given RNA sequence. [local] | Metzler & Nebel 2008 | http://www.cs.uni-frankfurt.de/~metzler/McQFold |
| RNAsubopt | Reads RNA sequences from stdin and calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). [local] | Hofacker 2004 | http://www.tbi.univie.ac.at/RNA |
| 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. [local] | Steffen et al. 2006 | http://bibiserv.techfak.uni-bielefeld.de/rnashapes |
| HotKnots | A heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. [local] | Renet al. 2005 | http://www.cs.ubc.ca/labs/beta/Software/HotKnots |
| Mfold | Mike Zuker's famous MFE RNA structure prediction algorithm. [remote] | Zuker 2003 | http://www.bioinfo.rpi.edu/applications/mfold |
| Sfold | Statistical sampling of all possible structures. The sampling is weighted by partition function probabilities. [remote] | Ding et al. 2004 | http://sfold.wadsworth.org/index.pl |
| RDfolder | RNA folding by energy weighted Monte Carlo simulation. [remote] | Ying et al. 2004 | http://rna.cbi.pku.edu.cn/ |
| 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.[remote] | Clote 2005 | http://clavius.bc.edu/~clotelab/RNALOSS |
| alteRNA | RNA Density Fold. Minimizes a linear combination of energy density and the total free energy for a given RNA sequence. [remote] | Aksay et al. 2007 | http://compbio.cs.sfu.ca/taverna/ |
Methods for secondary structure-based alignment
| Method | Description | Reference | URL |
|---|---|---|---|
| RNAforester | Compare and align RNA secondary structures via a "forest alignment" approach. | Reeder et al. 2006 | http://bibiserv.techfak.uni-bielefeld.de/rnaforester |
| MASTR | A sampling approach using Markov chain Monte Carlo in a simulated annealing framework, where both structure and alignment is optimized by making small local changes. The score combines the log-likelihood of the alignment, a covariation term and the basepair probabilities. | Lindgreen et al. 2007 | http://servers.binf.ku.dk/mastr/ |
| 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. | Witwer et al. 2004 | http://www.tbi.univie.ac.at/papers/SUPPLEMENTS/HXMATCH |
| Carnac | Comparative analysis combined with MFE folding. | Touzet 2007 | http://bioinfo.lifl.fr/carnac |
| RNAalifold | Folds alignments using a combination of free-energy and a covariation measure. Ships with the Vienna package. | Bernhart et al. 2008 | http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi |
| Foldalign | Structurally aligns two sequences using a light weight energy model in combination with RIBOSUM like score matrices. | Havgaard et al. 2007 | http://foldalign.ku.dk/ |
| RNAlishapes | RNAlishapes is a tool for RNA structure analysis based on aligned RNAs. | Voss 2006 | http://rna.cyanolab.de |
| RNAcast | The "consensus shapes" (RNAcast) method independently enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences. enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences, and for each sequence, the thermodynamically best structure which has this abstract shape. | Reeder & Giegerich 2005 | http://bibiserv.techfak.uni-bielefeld.de/rnacast/supplementary.html |
| RSmatch | Provides a lightweight approach to compare RNA structures, thereby uncovering functional structure elements. Compared with other tools for RNA structure comparison, RSmatch is fast, requiring quadratic time determined by the sizes of two given structures. | Liu et al. 2005 | http://exon.umdnj.edu/software/RSmatch |