Serves for the prediction of micro-RNA (miRNA) from small RNAseq data. miRDeep is a software for determining miRNAs, displaying RNAseq reads and the number of reads relative to the predicted pre-miRNA. It can provide the target prediction for both known and novel miRNAs expression levels, and display them in an interface showing each RNAseq read relative to the pre-miRNA hairpin.
A Web service for the analysis of ncRNA datasets derived from Illumina sRNA-Seq experiments. Starting with raw sequencing data, omiRas offers an efficient way to analyze differential expression of ncRNAs between two groups and to assign functions to differentially expressed miRNAs. MiRNA–mRNA interaction databases allow the user to construct networks of interesting miRNAs and mRNAs to identify miRNAs with implications in the development of differential gene signatures.
Provides small RNA (smRNA) sequencing in human cancer research. YM500 not only focuses on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). YM500 contains more than 11000 cancer-related smRNA and 10000 RNA-seq datasets. YM500, through its web interface, allows users to: (i) search for small RNA expression, (ii) search for miRNA Isoform, (iii) search for Novel miRNA, (iv) search for miRNA’s arm switching, (v) drive meta-analysis, (vi) drive survival analysis, (vii) drive cancer analysis, (viii) download their results.
An online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms. miREval 2.0 uses multiple published in silico approaches to detect miRNAs in sequences of interest. This tool can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data. miREval accepts up to 100 sequences of DNA or RNA in FASTA format. Comprehensive analysis is available for 31 species; partial analysis, including secondary structure prediction and alignment to known miRNAs, is still available for other species.
A web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection, and an API that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets, and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data.
Provides a comprehensive integrated pipeline for analyzing small RNA deep sequencing data. CPSS delivers analysis report from ncRNA quantification to miRNA target prediction and annotation of single and multiple datasets. The webserver supports more than 40 species. Each detailed result pages include a search function to find specific terms or values. For Gene Ontology (GO), pathway and protein domain analysis, users can optimize parameters and rerun analysis at each detailed result page.
A free web service that allows to study short read data from small RNA-seq experiments. DARIO provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The expression data and ncRNA predictions can be downloaded in the standardized BED format. We provide a script to locally convert SAM files and other mapping files to the BED format. The script is optimized to greatly reduce the amount of data that has to be uploaded to the DARIO server.
A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats.
Profile the content of a miRNA sequencing run. Given a set of aligned reads in 1 or more .sam files, produce an annotated version of the .sam where each read is given an annotation based on its coordinate. Additional summary information about the content of each sample is also generated, including miRNA species and other genomic features found.
Identifies phased small RNA clusters as ta-siRNA candidates by evaluating the P-values of hypergeometric distribution. pssRNAMiner is a web-based server which identifies ta-siRNA clusters as well as their potential phase initiators. This program requires that the user submit a set of small RNAs and specify one of listed transcript/ genomic libraries for mapping. It has the ability to identify potential phase-initiators based on the user input.
Allows to share and analyze aligned small RNA sequencing data. miRspring is a software document that aims to provide portability and a universal method to extract miRNA processing information from high-throughput sequencing (HTS) data sets. The software replicates the entire mapped data set and provides user-friendly way of presenting sequencing data along with inbuilt novel analysis tools that can globally assess the whole data set.
A small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data. NorahDesk utilizes the coverage-distribution of small RNA sequence data and thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. NorahDesk is particularly suitable for the prediction of piRNAs as it is the first program to "annotate by association": if novel transcripts form a thermodynamically stable secondary structure with already known piRNA transcripts, it is likely that the unannotated contigs are also piRNAs.
Analyses small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. The segmentSeq R package has been extended to identify methylation loci from high-throughput sequencing data from multiple conditions. A statistical model is then developed that accounts for biological replication and variable rates of non-conversion of cytosines in each sample to compute posterior likelihoods of methylation at each locus within an empirical Bayesian framework.
Predicts miRNA on both plant and animal data. miRCat is a part of the UEA small RNA Workbench and implements a new approach to differentiate miRNA candidates from background sequences, then applies novel filters on the candidate sequence alignments and secondary structure. The algorithm is performing well on animal datasets and also allows the detection of complex structures and even multiple miRNA loci within a single precursor in plants.
A framework python for the annotation and classification of the non-miRNA small RNA transcriptome. SeqCluster deals with sequences mapping onto multiple locations and permits a highly versatile and user-friendly interaction with the data in order to easily classify sRNA sequences with a putative functional importance.
Introduces a two-step approach to align RNA-seq read patterns with the aim of quickly identifying RNAs that share similar processing footprints. Overlapping mapped reads are first merged to blocks and then closely spaced blocks are combined to block groups, each representing a locus of expression.
A method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs). These sncdRNAs are often detected in sequencing data and observed as fragments of their precursor sncRNA. Using small RNA-seq read alignments, FlaiMapper is able to annotate fragments primarily by peak-detection on the start and end position densities followed by filtering and a reconstruction process.
A stand-alone package for systematically characterizing phasiRNAs and their regulatory networks. PhaseTank can identify phasiRNAs/tasiRNAs functional cascades (miRNA/phasiRNA --> PHAS loci --> phasiRNA --> target) with high sensitivity and specificity. By one command analysis, it generates comprehensive annotation and quantification of the predicted PHAS genes from any given sequences. PhaseTank has no restriction with regards to prior information of sequence homology of unrestricted organism origins.
Reconstructs the surface of structural potential using an algorithm for Z-score evaluation. RNASurface introduces an intuitively clear definition of locally optimal segments as peaks in the surface of structural potential. This application allows users to identify structured domains comprising the region. This method can be useful for (i) preprocessing during de novo search for regulatory and noncoding RNAs, (ii) accurate definition of ncRNA boundaries and (iii) correlation of genome-scale structural potential with other genomic features.
Analyzes smallRNA-Seq data. iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). It implements specific computational modules to analyze PIWI-interacting RNAs (piRNAs), predicting novel ones and identifying the RNA targets. The pipeline can provide a comprehensive analysis of different classes of small non-coding RNAs (sncRNAs). iSmaRT can provide a detailed analysis of miRNA and piRNA differentially expressed and of piRNA-mRNA interactions.
Allows identification of candidate small interference RNA (siRNA) target sites. siRNA Target Finder finds the small interference RNA (siRNA) target sites in messenger RNA (mRNA) sequence. The software can be used for identifying candidate siRNA target sequences within complementary DNA (cDNA). The program is hosted on a secure Web server to protect users’ privacy.
Performs novel noncoding RNA (sncRNA) detection. RNAdetect jointly analyzes a set of aligned sequences, obtained from comparative genome analysis, to extract predictive features and predict the presence of potential ncRNAs in the given sequences, using a support vector machine (SVM). The software incorporates features based on the concept of generalized ensemble defect and n-gram models.
Allows to create web sites dedicated to non-protein-coding RNA (ncRNA) prediction, annotation and analysis. RNAspace is an environment that allow users to run a variety of tools in an integrated and flexible way. RNAspace is focused on the integration of complementary ncRNA gene finders. It also offers a set of tools for the comparison, visualization, edition and export of ncRNAs candidates. Predictions can be filtered according to a large set of characteristics.
Detects mature miRNAs directly from next generation sequencing read data, without any need of reference/genomic sequences. miReader was tested over wide range of species, and the presented approach achieved high accuracy for all the target species. Using the same approach, 21 novel mature miRNA duplex candidates were identified for a plant species whose genome has not been sequenced yet and there is negligible miRNA data reported for this species in miRBase. This has clearly demonstrated clearly that in spite of unavailability of genomic sequences, the presented tool, miReader, could accurately identify the mature miRNAs directly from small RNA sequencing data.
Identifies miRNA candidates with high accuracy and stable performance over wide range of species. Biologically relevant novel features like miRNA specific mature miRNA guided structural profile matrices and structural triplet density variation profiles with respect to position have been introduced to derive a superior and stable performance. An ensemble machine learning methodology, bootstrap aggregating (BAGging), has been implemented. It employs complementary classifiers like support vector machine (SVM), naive Bayes (NB) and best first decision trees (BFTree) to build the final classifier models for large number of species, enhancing the performance strongly. An NGS module has been built to find miRNA precursor candidates, using Illumina read data. The process of miRNA candidate detection requires large volume of sequence data scanning, which makes it dependent upon extensive computing.
Offers a platform dedicated to the detection and prediction of PIWI-interacting RNA (piRNAs), including piRNA clusters, from small RNA sequencing data. PILFER is an open source program that uses both expression and spatial information of the piRNA hits for its clusters prediction. The application first determines regions of the genome with a high expression value from the mapping file and then uses a sliding window approach to form a cluster around the localized region.
Extracts microRNAs (miRNA) expression profiles from sequencing reads generated by second-generation sequencing. miRExpress contains miRNA information from miRBase and reveals miRNA expression profiles by aligning sequencing reads against the sequences of known miRNAs. The software supports that sequences are aligned with miRNA precursors. It can be used to determine miRNA expression profiles when genomic sequences are unavailable, and to find novel miRNA candidates by aligning reads with sequences of known miRNAs of various species.
An integrated package for identification of plant miRNA from RNA sequencing data. miRPlant visualizes novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. This software can be easily used by biologists with limited bioinformatics skills, with possibility to use other species. It is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs.
A tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. miRA is particularly suited for organisms with no existing miRNA annotation, or without a known related organism with well characterized miRNAs. Moreover, miRA has proven its ability to identify species-specific miRNAs. miRA is flexible in its parameter settings, and produces user-friendly output files in various formats (pdf, csv, genome-browser-suitable annotation files, etc.).
Produces accurate miRNAs expression level quantification and both isomiRs and miRNA-mRNA interaction sites precise classification. isomiR-SEA exploits a miRNA specific alignment algorithm that is able to correlate the encountered mismatches with their positions on the miRNA sequence. It can be useful for analyses of large datasets. This tool allows users to design wide miRNAs studies.
Offers a method for organizing precursor non-coding RNA (ncRNA) sequences according to their similarity with transposable elements (TE) sequences. ncRNAclassifier provides a graphical interface for computing the number of occurrences of the candidate, the number of chromosomes within occurrences and the distance between them. Then, it generates a consensus sequence from the ten most similar occurrences to the input sequence and checks its correspondence to a TE through RepBase database.
A tool for miRNA prediction that requires only sRNA datasets as input. Mature miRNAs are predicted from such datasets through a multi-stage process, involving filtering, miRNA:miRNA* duplex generation and duplex classification using a support vector machine. Tests on sRNA datasets from model animals demonstrate that the tool is effective at predicting genuine miRNA duplexes, and, for some sets, achieves a high degree of precision when considering only the mature sequence.
Allows users to determine microRNA using integrated evidence. miPIE consists of a classification method for miRNA prediction by integrating both sequence and expression-based features. Furthermore, it utilizes mirDeep2’s pre-processing step to identify putative pre-miRNA regions.
Performs simultaneous analysis of bacterial small RNAs (sRNAs) derived from a variety of genomic features. TEsmall facilitates the discovery of intriguing biological phenomena otherwise masked by insufficient annotation of repetitive genomic elements and allows their incorporation into downstream differential analysis. Users can simultaneously map and annotate many types of sRNAs including structural RNAs, microRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs).
Exploits differential distribution of k-mer motifs among ncRNAs with respect to the background genome sequence. smyRNA computes log-likelihood scores for a specific sequence to be in a potential ncNRA sequence. It assists in identification of subsequences of a genome that can then be considered as a candidate ncRNA gene. This application was able to identify a significant fraction of known Shigella flexneri ncRNAs while returning only a small number of false positives.
Processes small-RNA data from next-generation sequencing (NGS) platforms such as Illumina and SOLID. sRNAbench can analyze an unlimited number of genomes simultaneously without the need to pool all sequences into a single index. Users can perform adapter trimming and extensive profiling of all microRNA sequences and length variants. This tool is available as a web application and as a standalone program with full parameter space and more customized analysis steps.
Allows investigation of non-coding RNA (ncRNA) sequences, expression levels, differentially expressed ncRNAs and miRNA-targeted genes and their functional annotation. mirTools provides several modules including (1) a single case to detect various types of known and novel ncRNAs and perform functional annotation of the miRNA-targeted genes for a single sample, (2) two cases and group cases to identify differentially expressed ncRNAs between or among samples, and (3) re-analysis to run previously submitted data with adjustable parameters.
Incorporates the mechanisms of miR biogenesis and includes additional criteria regarding the prevalence and quality of small RNAs arising from the antisense strand and neighboring loci. miRTRAP was developed for the systematic prediction of miRNAs from high-throughput sequence data. In contrast to most current methods, it utilizes a system of binary decisions based on known biochemical mechanisms of miRNA biogenesis.
Identifies all potential regulatory ncRNAs that can establish stable joint structures with a query mRNA. pRuNA is a RNA search engine that retains only the most likely non-coding RNA (ncRNA) candidates for forming a stable joint structure with the query mRNA. It recognizes all pairs of 5-mer motifs from the ncRNA loop sequences that are complementary to a pair of 5-mer motifs in the loop sequences of the query mRNA. Moroever, pRuNA is part of taveRNA, a web server package.
A prediction tool which is based on an integrated adaptive boosting method and contains two modules. The first module named mirExplorer-genome was designed to de novo predict pre-miRNAs from genome, and the second module named mirExplorer-NGS was used to discover miRNAs from NGS data. A set of novel features of pre-miRNA secondary structure and miRNA biogenesis has been extracted to distinguish real pre-miRNAs from pseudo ones.