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.
Serves for differential expression analysis of miRNAs derived from small RNA-Seq data. omiRas offers specific functionalities such as the annotation, comparison and visualization of interaction networks of non-coding RNAs (ncRNAs) derived from next-generation sequencing experiments of two different conditions. Furthermore, users can submit several raw sequencing data. This program then presents the results as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables, and (ii) an interactive network visualization of user-selected miRNAs and their target genes.
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.
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.