1.- In silico miRNA prediction

The selected applications are designed for the computational prediction of miRNA genes within genomic sequences. They use several  algorithms, including neural networks and SVM. The majority of these classical applications have been discontinued along years because of the emerging role of NGS techniques. However, these applications can still be useful for the prediction of miRNA genes when working with "exotic" and new genomes. Moreover, these tools could be also useful in prediction of putative new miRNA genes emerging from somatic mutations.

App/WEB	COMMENTS	Reference
SSCprofiler	Human genome scanner for the prediction of putative miRNA genes. By selecting the chromosome number and the start and end nucleotides, it is possible to scan specific genomic regions for miRNA genes.	PMID: 19324892
MapMi	A tool designed to locate miRNA precursor sequences in existing genomic sequences, using potential mature miRNA sequences as input. After searching the genome for the provided mature sequences, these hits are extended and classified taking into account major structural properties of known miRNA precursors.	PMID: 20233390
MiRscan	Classical miRNA prediction server by the Bartel's lab.	PMID: 15317971
Vir-Mir-db	Viruses are capable of encoding miRNAs and using them to repress host genes. Thus, identifying potential miRNAs in all viral genomes would be valuable to virologists who study virus-host interactions. This database contains results of 2266 viral genome putative miRNA hairpins and identified 33691 hairpin candidates in 1491 genomes.	PMID: 17702763
mirDeep*	miRDeep* and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). It is a software for local installation, however it has a graphical interface.	PMID: 23221645
miRQuest	Identification of miRNAs in plants and animal genomes by integration of several prediction tools.	PMID: 27050998
SplamiR	It is the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem-loop structures, identifying putative mature miRNAs.	PMID: 21421552

 

2.- RNA structure

These servers are designed for the prediction and analysis of 2D and 3D structural information extracted from RNA sequences. They can be very useful to analyze local miRNA effects over their cognate targets.

App/WEB	COMMENTS	Reference
Vienna servers	Impressive collection of web utilities for calculation and analysis of RNA secondary structures.	PMID: 18424795
RNAshapes Studio	The RNA shapes studio comprises four RNA secondary structure prediction tools, which make heavy use of shape abstraction. An abstract shape is a mathematically well defined coarse grained view of an RNA structure, supporting the user to focus only on "interesting" structural features. It contains many utilities for single RNA or hybrid RNA molecule folding.	PMID: 25273103
Sfold	Statistic analysis of RNA folding, and rational design tools for nucleic acids.	PMID: 24803672
PKiss	Localization of pseudo-knots in RNA sequences.	PMID: 25273103
CentroidFold	CentroidFold predicts an RNA secondary structure from an RNA sequence. FASTA and one-sequence-in-a-line format are accepted for predicting a secondary structure per sequence. It also predicts a consensus secondary structure when a multiple alignment (CLUSTALW format) is given.	PMID: 27131356
RNAbor	Compute the number and Boltzmann probability of the set of secondary structures of a given RNA sequence at base pair distance δ from a given structure.	PMID: 17526527
iFold_RNA2	Interactive RNA folding simulations by discrete molecular dynamics calculations.	PMID: 25910700
MFold	Prediction of melting profiles for nucleic acids, including DNA and RNA.	PMID: 17702763