The study of RNA structure has developed a distinct set of computational tools designed explicitly for RNA applications. Frequently, different regions of the same RNA strands fold together via base pair interactions to make complicated secondary and tertiary structures that are essential for different biological function.

Tool Names




MiRAlign is designed to find new miRNAs using both sequence information and structural characteristics of known miRNAs. It detects new miRNAs based on both sequence and structure alignment.



ProMiR (ver 1.0): Probabilistic co-learning model for miRNA gene finding. It combines both sequential and structural characteristics for miRNA genes in a probabilistic framework, and simultaneously decides both whether or not a miRNA gene is present.



Mirscan is intended to identify the most microRNA-like hairpin sequences from an arbitrary set of candidates.


ProMiR (ver 1.0): Probabilistic co-learning model for miRNA gene finding. It combines both sequential and structural characteristics for miRNA genes in a probabilistic framework, and simultaneously decides both whether or not a miRNA gene is present.

ERPIN (Easy RNA Profile IdentificatioN)

ERPIN is a software program for RNA motif identification. ERPIN reads a sequence alignement and secondary structure, and automatically infers a statistical "secondary structure profile" (SSP). An original Dynamic Programming algorithm then matches this SSP onto any target database, finding solutions and their associated scores.


It classifies the real and pseudo microRNA precursors using random forest prediction model with combined features.



It recognizes the miRNA precursors in Comparative Genomics Data. It is available as a standalone program and as web based program.



It is a comprehensive tool, easy to use and very informative.



A computational pipeline called MIRFINDER identifies conservedhairpin structures in the genomes of A. thaliana and Oryza sativa and subsequently applies several filters, based on core features derived from known miRNAs.

mfold software


mfold for RNA folding was developed in the late 1980s. It is a web server for nucleic acid folding and hybridization prediction. The core algorithm predicts a minimum free energy ?G as well as free energies for folding that must contain any particular base-pair.




RNAsoft is a collection of online services for the computational prediction and design of RNA/DNA structure. Three programs are currently available in RNAsoft are Pair fold, comb fold and RNA designer.



RNAz is used for predicting structurally conserved and thermodynamically stable RNA secondary structure in multiple sequence alignment. It makes use of the support vector machine classification procedure, which estimates a class-probability which can be convenient overall score.

VIENNA RNA package


Vienna RNA package has C code library and many stand alone programs for the prediction and comparison of RNA secondary structures.The mostly used function in the package is RNA secondary structure prediction through energy minimization.



XRNA is secondary structure display software. XRNA is a Java based collection of tools for the creation, annotation and display of RNA secondary structure diagrams.

CONTRAFOLD (conditional training for RNA secondary structure prediction)

This method is based on conditional long linear models. It integrates most of the thermodynamic features in models and gives highest single sequence accuracy values till now.




It creates a map of the structure in a tree like domain. It delivers thermodynamically best structure for each sequence which has common shape.



Alifold predicts consensus secondary structures for the set of aligned RNA and DNA sequences. It is offered by the Vienna RNA package.



EvoFold is a comparative method for identifying functional RNA structures in multiple-sequence alignments. It is based on a probabilistic model-construction called phylo-SCFG and exploits the characteristic differences of the substitution process in stem-pairing and unpaired regions to make its predictions.


This tool is based on comparative genome sequence analysis. And it detects conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures

Xrate (

Xrate is an interpreter for phylo-grammars (it is a stochastic grammar whose terminals are alignment columns, typically generated by evolving a continuous-time Markov process on a phylogenetic tree).


MSARi (Multiple sequence alignments for statistical detection of RNA secondary structure)


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



This program uses a scoring matrix, which is based on the parameters of the siRNA design for evaluating the inhibitory potency of siRNAs.


BLOCK-It RNAi designer

This program design synthetic siRNA, stealth RNA and shRNA. It utilizes a highly effective, proprietary algorithm and can be used for efficiently designing different kinds of RNAi molecules.



Sfold is based on patent-pending algorithm for RNA folding, target accessibility prediction, and rational design of RNA targeting nucleic acids.


Dharmacon siRNA Design Center


The siDESIGN Center is an advanced, user-friendly siRNA design tool, which significantly improves the likelihood of identifying functional siRNA.


ERPIN (Easy RNA Profile Identification)


It is program for RNA motif search and it does not require users to write complex descriptors before starting of a program and instead of that it reads a sequence alignment and secondary structure and draws an inference of statistical secondary structure profile.

INFERNAL (inference of RNA alignment)


It is a program which search DNA database for RNA structure and sequence similarities. It is implements a covariance model, which is a special type of stochastic context free grammar.

PHMMTS (pair hidden markov models on tree structure)


It is an extended version of pair hidden markov model. This program does a local alignment on an unfolded sequence by a folded structure.



This program searches a database for homologous RNAs. It uses SCFG algorithm to score secondary as well as primary sequence alignment.



This software speeds up the CM (covariance model) by implementing various techniques. The technique is “ML-heuristic” where a heuristic method is used to speed up the CM.