Discovers genes involved in a biological process. RNAiCut employs the connectivity of subgraphs of protein-protein interaction (PPI) networks to find score thresholds from functional genomic data. It allows hit-list gene selection with orthogonal datasets. This tool calculates the edge count of induced subgraph and determines the P-value of finding a PPI subgraph. It is useful for functional genomics research.
Identifies, predicts and characterizes noncoding RNAs (ncRNAs). incRNA is a machine learning framework which integrates sequence, structure, and expression data. The software was used, with data from the modENCODE consortium, to separate known C. elegans ncRNAs from coding sequences and other genomic elements and find more than 7000 novel ncRNA candidates, among which more than 1000 were located in the intergenic regions of C. elegans genome.
Finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, etc.) by computing all semi-global alignments. GotohScan is a computationally sensitive full dynamic programming approach. Thus, the query sequence is never truncated or split into sub-sequences, but always mapped to the database over its complete length. The alignment is computed via the Gotoh-alignment algorithm using affine gap costs.
A clustering method that efficiently identifies noncoding RNA (ncRNA) elements in a bacterial genome. This web server enables users to retrieve RNA-rich clusters from any genome in a list of 1000+ sequenced bacterial genomes. RNA-rich clusters can be viewed separately or, alternatively, all tiles from RNA-rich clusters can be contiged into larger elements and retrieved at once as a CSV or GFF file for use in a genome browser or comparison with other predictions/RNA-seq experiments.
Performs comprehensive ncRNA profiling and differential expression analysis on deep sequencing generated data. RandA reveals the complexity of the ncRNA repertoire in a given cell population. It maps the reads against the newly formed database using a Burrows–Wheeler transform based alignment tool summing the number of reads that mapped uniquely to each of the annotated ncRNA sequence. The tool produces a table comprising of all the mapped ncRNAs in a given sample.
Predicts the pathogenicity of single nucleotide substitutions in human mitochondrial tRNA (mt-tRNA) variations. PON-mt-tRNA arranges the variations with the maximum likehood (ML) method and has a 2-fold importance for diagnosing the pathogenicity of mt-tRNA variations. It classifies variations into five classes: neutral, likely neutral, pathogenic, likely pathogenic and variants of uncertain significance.
Identifies active microRNA transcription start sites (miRNA TSSs) from nascent transcriptomes. MirSTP provides accurate TSS prediction for human intergenic miRNAs at a high resolution by using characteristic bidirectional transcription signatures. It can be applied to any cell line or condition with available Global nuclear run-on (GRO)/precision nuclear run-on sequencing (PRO-seq) data.
Analyzes miRNA next generation sequencing (NGS) data. MiRMaster performs the most frequently requested applications and aims to help in searching for novel miRNA candidates, quantifying miRNA expression and identifying isoforms and variants of miRNAs. Besides, the application can proceed the mapping of non-human small RNA reads against the NCBI RefSeq collection of bacterial and viral genomes to detect contaminations, infections or exogenous miRNAs.
Predicts siRNA off-target interactions and enables off-targeting potential comparisons between different siRNA designs. siRNA off-target discovery pipeline can predict the off-target transcripts and compute the off-targeting potential of a given siRNA in human. This pipeline can easily be tuned for any other organism by simply replacing the input data. This tool is able to calculate siRNA off-targeting potentials on an entire human genome/transcriptome in the time scale of hours thanks to the large-scale prediction capabilities of RIsearch.
Infers gene-specific contributions to phenotypes in RNA interference screens. PheLiM proceeds by integrating predictions of on- and off- target small interfering RNA-(siRNA) induced down-regulation. It can discover validated targets and related potentially new regulators from different screens that calculated several phenotypes. This tool achieves better results when the prediction accuracy on seed-disjoint validation datasets are maximized.
Allows users to determine long non-coding RNA (lncRNA) interactions using four models for lncRNA regulation. LongHorn is a pan-cancer analysis of lncRNA regulatory interactions. This tool is able to detect four models for lncRNA regulation: decoy (binds and inhibits the activity of effectors); co-factor (binds proximal promoters of protein-coding genes and alter their regulation by transcription factors (TFs)); guide (simplifies regulation of protein-coding genes by TFs); and switch (alters the activity of TFs and RNA-binding proteins (RBPs) across multiple targets).
Supports the translation of micro-RNAs (miRNAs). miRNACon is a web application that permits users to test individual miRNAs or miRNA signatures for likelihood of being influenced. This tool proceeds in five steps where researchers have to: (1) select miRBase version; (2) select miRNA identifier; (3) enter parameters related to age; (4) select probe type; and (5) place their input for realizing the computation.
Allows users to score high two Infernal covariance models. CMCompare is an extendable polynomial-time algorithm that furnishes information for: (i) determining the high discriminative power of a model against other ones; (ii) localizing which regions of the model overlap with another; (iii) obtaining a natural similarity score for RNA families. It aims to help in selecting models as well as check relationships between them.
Detects genes and other potentially functional sequences that may be missed by standard ORF-calling, RNA finding, and pattern matching software. Tricross produces a multi-way cross comparison of three sets of sequences, determine which are conserved in all three sets, and produce a graphical representation as well as alignments of all sequence triples found.
Identifies the binding sites of RNA molecules. RBind transforms the RNA tertiary into a network, where nucleotides are nodes, and their non-covalent interactions with each other are the edges. It recognizes binding sites by determining the degree values for short-range binding cavity and closeness values for long-range allosteric effect. This tool is useful to find critical nucleotides for binding.
Enables researchers to predict the origin site of tumor samples of their interests. MMCOP is a web-server that consists of classifiers based on Illumina 450k DNA methylation (DNAm) profiles and microRNA (miRNA) expression. 14 tissues for miRNA expression profiles are supported by the software, as well as the same number for DNA methylation profiles. The software was tested using seven DNAm datasets in GEO.
Resolves ambiguous mappings on the basis of a statistical model that can be customized by the user. bcSeq is an open source R package for mapping reads from high-throughput shRNA and sgRNA sequencing assays based on a default or a user-defined Phred score-based probability model. It accommodates sequences of varying lengths and provides the option of using Hamming or edit distance. It can also tolerate mismatches, internal insertions and deletions.
Permits users to detect ping-pong cycle activity in small RNA-Seq data. PingPongPro is an application that locates sites of piRNA-mediated cleavage and identifies transposons suppressed through the ping-pong cycle. This method takes additional covariates into account and auto-tunes its parameters to the data. It is built on the next-generation sequencing (NGS) analysis library SeqAn.
Offers a platform for forecasting miRNA essentiality. miES provides an algorithm, usable through both a desktop program or as a web-hosted application, assisting users in selecting miRNAs for further experiments. This software consists of two main panels allowing the prediction as well as the querying of miRNAs of interest from the miRbase or the miRCarta repositories.
Performs an automatic recognition of blocks of reads. blockbuster is based on an algorithm that replaces each read by Gaussian profile centered at the midpoint of the read. The application can be employed to verify miRs and miRs* position between annotation and short-read data as well as for identifying their associated expression levels. The software accepts files from the segemehl software and can be used in conjunction with it.
Models combinatorial perturbations via probabilities and processes network reconstruction from combinatorial gene knockdown data. pcNEM is based on nested effects models (NEMS) and deals with combinatorial off-target effects in a probabilistic manner. It measures the error rates and assesses the quality of the data or potential model misspecification. It can also determinate equivalent directed acyclic graphs (DAG) structures from nested data.
Provides a random forest classifier. TOC uses: (1) Translational efficiency (TE); (2) inside versus outside (IO); (3) fraction length (FL) and (4) disengagement score (DS) to proceed. It integrates intrinsic transcript information, such as sequence and location of ORFs, with external data, such as ribosome profiling and expression levels derived from RNA-seq. This tool is able to refine the classification of putative lncRNAs.
Identifies tumor-associated function of thousands ceRNA genes as a whole. MACPath groups ceRNA relationships by competing-endogenous pathways (cePathway). It permits users to calculate dysregulated cePathway relationships between cancer and normal cells. When applied to TCGA breast cancer data, this method also discovers thousands of lost and gained cePathway relationships, which provide biological insights into ceRNA regulations during tumorigenesis.
Deduces genome-wide cancer-associated competing endogenous RNA (ceRNA) interaction networks. Cancerin proposes an approach which is able to consider information from both putative miRNA-RNA interactions and miRNA/RNA expression profiles as well as data derived from transcription factors, copy number alteration, and DNA methylation. This package was tested on breast, kidney and head neck cancer.
Predicts pathogenicity of novel mitochondrial tRNA variant. MitoTIP is designed to analyze novel or infrequently observed single nucleotide variants in tRNA sequence and to separate benign and pathogenic variants. It uses the structure of the MITOMAP database for accessing to updated information. The pathogenicity scoring results can be used as a starting point for the evaluation of newly observed tRNA variants.
Allows users to do a systematical search for the natural antisense transcripts (NATs) in the organisms without reference genomes. NATpipe is a pipeline enables users to identify the phase-distributed nat-siRNA loci within the perfectly annealed regions of the NAT pairs based on sRNA and degradome sequencing. This application also performs strand-specific mapping of the degradome signatures onto the NATs with phased nat-siRNA loci if users have degradome-seq data.
Facilitates lincRNA discovery and characterizes aspects of lincRNA evolution. Evolinc is a two-module pipeline. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analyses workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species.
Predicts numerical efficacy of siRNAs targeting different genes of human viruses. VIRsiRNApred is a viral siRNA efficacy prediction algorithm that can classifies a siRNA as effective/non-effective. It offers an updated list of the experimentally validated siRNAs along with their numerical inhibition values reported in scientific literature. It also offers predicted siRNAs against important genes of HIV, Influenza, HCV, HBV and SARS.
Pinpoints small regulatory RNAs (sRNAs) homologs in complex genomic databases starting from a single sequence. GLASSgo is a web application that directly displays the predicted homologs ready for downstream analyses. The sensitivity of this tool can be customized and be enhanced without altering the specificity by re-running GLASSgo with a total true positive (TP) that possesses a low pairwise identity to the query. This software’s aim is to ameliorate the high-throughput functional classification of sRNAs.
Allows to compile miRNA data for given target genes from public databases. MIRNA-DISTILLER implements TargetScan, microCosm, and miRDB, which may be queried independently, pairwise, or together to calculate the respective intersections. Data are stored locally for application of further analysis tools including freely definable biological parameter filters, customized output-lists for both miRNAs and target genes, and various graphical facilities. The software, a data example file and a tutorial are freely available for download.
Helps in analysis of the high-through sequencing (HTS) data. CSZ is an efficient platform for characterizing small RNAome from the deep sequencing data in zebrafish. This method was developed to demonstrated an sRNA class transition from piRNAs to miRNAs as development proceeds. It also includes the algorithm ZmirP, a module of CSZ used for further filtering potentially false positive hits.
Permits high-quality sequence annotation without specific knowledge of the field. Unitas allows subsequent analysis of non-template 3′-nucleotides. It enables researches to elucidate possible functions of these cryptic RNAs by first of all spotting them in sncRNA transcriptomes. This tool is suitable for the detection of particularly low abundance phasiRNAs and their source loci. Its sensitivity depends far less on the amount of background reads.
Identifies miRNAs that may be involved in the association between single nucleotide polymorphisms (SNPs) and an alcohol phenotype. This approach can detect the various mechanisms that affect traits of interest through the modification of miRNA expression. This tool can be used to detect targets for miRNA therapeutics and pathways in which these genes are enriched and associated with alcohol-related traits.
Infers regulation relationship between miRNAs and mRNAs in plant using small RNA sequencing data and RNA sequencing data. PlantMirnaT is a comprehensive system for miRNA target inference deploying many methods in a single framework, such as de novo sequence mapping algorithm for plant and the regression based model optimization. This system is designed for sequencing data and also for plant specific characteristics.
Performs selection of efficient small interfering RNA (siRNA) candidates. si-shRNA Selector is a program that generates siRNA candidate oligonucleotides of user defined length. The software is suitable for mammalian short hairpin RNAs (shRNA) design, because the database from which algorithm was designed includes experiments performed in mammalian cell cultures.
Identifies microRNA (miRNA) that are differentially expressed between two different groups of samples. miRtest combines high-throughput miRNA and mRNA expression data to ameliorate the power of testing either data type individually. This method decreases the number of false positives found in gene set testing. It also finds miRNAs that show an effect either in their own expression.
Utilizes two layers of support vector regression (SVR) to predict the efficacy of a small interfering RNA (siRNA). siPRED is based on various characteristic methods in the first layer and fusion mechanisms in the second layer. Characteristic methods were constructed by support vector regression from three categories of characteristics, namely sequence, features, and rules. In siPRED, the prediction of siRNA efficacy through integrated methods was better than through any method that utilized only a single method. siPRED is freely available on the web.
Assists users in identifying ncRNA in next-generation sequencing (NGS) data sets that lack reference genomes. RNA-CODE is a ncRNA classification tool for short reads. It classifies reads into different types of ncRNA families. The classification results can then be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively.
Provides a meta-predictor that was developed by integrating a set of non-linear transformations with meta-strategy. mirMeta contains five individual predictors: MiPred, MIReNA, miRPara, ProMiR, and triplet-SVM. The outputs of five individual predictors are processed using preprocess-III, which includes numericalization, normalization, distribution-shift of ProMiR predictions, and principal component analysis (PCA) transformation of all five individual predictions.
Sorts features based on a criterion that involves all other features. UFFizi is based on the unsupervised feature filtering (UFF) algorithm, that employs an entropy measure applied to singular value decomposition (SVD). It employs information contained in the singular values in order to select the features. This tool can serve to discover rare events in the dataset or filter faulty instances before proceeding with further analysis.
Identifies Long Non-Coding RNA Identification. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. It provides an option for the users to train a classifier on users’ own datasets, which greatly facilitates the researches who are interesting on some poor-explored species. The tool outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK.
Allows users to detect guide strands of miRNAs. RISC binder offers a computational approach to distinguish miRNA and miRNA* strands. The web application uses a support vector machine (SVM) method and was trained by using a dataset of over 300 miRNAs and miRNAs*. It is able to perform its forecasting according two different modes: (i) structure & sequence based analysis and (ii) a single sequence based prediction.
Provides a risk prediction model with the aim of assisting users in complex diseases analysis. The package provides an approach merging gene expression data and microRNA (miRNA) expression data. It employs a bipartite graph derived from correlations between miRNA, gene expression data and target prediction information coupled with a CoxBoost model. The software was applied to the study of the risk of biochemical relapse for prostate cancer patients.
Allows users to predict and describe ncRNA transcripts in bacteria. NOCORNAc is a standalone software that can perform strand-specific transcript predictions that can be applied to intergenic regions as well as cis-encoded asRNA transcripts. It accepts as input either the whole chromosome or the coordinates of putative ncRNA. Besides, the application includes additional features such as a way for searching known RNA motifs from the Rfam database.
Recognizes novel long non-coding RNAs with the obtained signatures from fasta and gtf formats. Islnc is a web tool that was applied on a study and reveals different signatures in human, mouse, and zebrafish. It permits to highlight that some features are shared among species, while others tend to be species-specific. This method improves the prediction performance, in terms of area under precision and recall curve, by 1 to 24%, depending on the species and on the signature.
Allows to detect multi-disease associated co-functional microRNA pairs. PreDisRNA focuses on the detection and prioritization of multi-disease associated co-functional miRNA pairs. This tool presents a method which is based on two ideas: (1) the first is the construction of a set of reliable negative samples of disease-miRNA association through miRNA expression comparison between control and diseased subjects, (2) and the second is the use of precomputed kernel matrix for support vector machines (SVM).
Automates the process of generating mutant sequences and enables selective disruption of specified microRNA (miRNA). ImiRP can generate miRNA target site mutations in any sequence of interest and deal with illegitimate miRNA target site creation. This software suits for investigating regulation of single mRNA 3’UTR by multiple miRNAs. It is available as a web interface and a downloadable version.
Allows to study the unique nature of miRNAs. QuickMIRSeq presents a high redundancy of miRNA reads and includes joint mapping of multiple samples in order to lower computational time. It also contains the strand information in the alignment step for more accurate quantification. It filters out potentially arising from background noise in order to set up a better detection.
Provides a user interface for various cancer types of miRNA-mRNA expression data with significant interaction pairs. MMiRNA-Viewer is a graph visualization tool that supports dynamic queries to help users in searching meaningful cancer biological findings. This application can calculate and plot the correlation of expression for mRNA-miRNA pairs across samples or over a time course using a pre-defined correlation cutoff and prediction confidence.