| miRanalyzer is a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features. Alignments are now based on the ultrafast short-read aligner and 31 genomes, including 6 plant genomes, can now be analyzed. Differences between plant and animal microRNAs have been taken into account for the prediction models and differential expression of both, known and predicted microRNAs, between two conditions can be calculated. |
| Detection of known and prediction of new microRNAs |
| "DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. |
| Recognition of known and prediction of novel microRNAs |
| deepBase v2.0 decode evolution, expression patterns and functions of diverse ncRNAs across 19 species. deepBase v2.0 has been updated to provide the most comprehensive collection of ncRNA-derived small RNAs generated from 588 sRNA-Seq datasets. Moreover, we developed a pipeline named lncSeeker to identify 176 680 high-confidence lncRNAs from 14 species. By combining expression profiles and functional genomic annotations, we developed lncFunction web-server to predict the function of lncRNAs based on protein-lncRNA co-expression networks. |
| Annotation and discovery of small RNAs and Long non-coding RNAs |
| miRCat identifies mature miRNAs and their precursors. Users upload a FASTA file of sRNA sequences, which are mapped to a plant genome using PatMaN and grouped into loci. To enrich for miRNA candidates, a number of empirical and published criteria for bona fide miRNA loci are applied by the software details listed on the tool's website. The program searches for a two-peak alignment pattern of sRNAs on one strand of the locus and assesses the secondary structures of a series of putative precursor transcripts using the RNAfold programs. |
| predict miRNAs from high- throughput RNA sequencing data without requiring a putative precursor sequence |
| miRExpress for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. The utility of miRExpress demonstrate in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species. |
| Recognition of new or known miRNAs from high-throughput sequencing |
| miRProf determines normalised expression levels of sRNAs matching known miRNAs in miRBase. miRProf can also quickly and easily compare miRNA expression levels across multiple samples. miRProf requires a set of sRNA samples and a genome file for input. The paths to the files representing the samples and the genome are entered at the top of the main dialog box. In addition, miRProf can be configured in a number of ways, which are described in the following paragraphs. |
| Determine known miRNA expression profile in a large-scale data set |
| mirTools 2.0 includes the following new features. (1) mirTools 2.0 allows users to detect and profile various types of ncRNAs, such as miRNA, tRNA, snRNA, snoRNA, rRNA, and piRNA. (2) mirTools 2.0 allows users to identify miRNA-targeted genes and performs detailed functional annotation of miRNA targets, including Gene Ontology, KEGG pathway and protein-protein interaction. (3) mirTools 2.0 allows users to detect differentially expressed ncRNAs between two experimental groups or among multiple samples. |
| ncRNA profiling and discovery based on high-throughput sequencing Including Gene Ontology, KEGG pathway and protein protein interaction |
| SiLoCo identifies sRNA loci on plant genomes from two sRNA datasets, which can be uploaded by the user and/or selected from publicly available datasets. SiLoCo maps sRNA sequences to the genome using PatMaN and weighs each sRNA hit by its repetitiveness in the genome. Loci are defined by a minimum number of sRNA hits to a region and a maximum ‘gap’, i.e. absence of sRNA hits, between them. Hit counts are normalized to the total number of genome-matching reads in each sample to make them comparable. |
| small RNA locus comparison |
| BioVLAB-MMIA is compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). BioVLAB-MMIA-NGS deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of a miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy. |
| System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs with targeting information computes DEGs targeted by DEmiRNAs |
| CPSS (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. Small RNA NGS data can be submitted to this server with analysis results being returned in two parts: (i) annotation analysis, which provides the most comprehensive analysis for small RNA transcriptome, including length distribution and genome mapping of sequencing reads, small RNA quantification, prediction of novel miRNAs, identification of differentially expressed miRNAs, piwi-interacting RNAs and other non-coding small RNAs between paired samples and detection of miRNA editing and modifications and (ii) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of gene ontology terms, signalling pathway involvement and protein-protein interaction analysis for the predicted genes. |
| Annotate and functionally analyze microRNAs from NGS data |
| DARIO is a web service that allows to study short read data from small RNA-seq experiments. It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. |
| Recognition of known and prediction of novel microRNAs |
| isomiRex identifies isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. The open-access web-platform is not restricted only to NGS sequence dataset from animals and potentially analyzes a wider dataset for plants, animals and viral NGS dataset supporting miRBase. The platform can handle the bloated amount of the read counts and reports the annotated microRNAs from plant, animal and viral NGS datasets. isomiRex also provides an estimation of the the isomiRs, of miRNAs with higher copy number relative to their mature reference sequences indexed in miRBase. |
| Known miRNA identification Differential expression IsomiRs identification |
| MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. MAGI’s salient features are (i) transfer of large input files, (ii) rapid prediction of microRNA target genes leveraging parallel computing, (iii) all-in-one analytics with novel feature extraction and (iv) interactive visualization and exploration of results. |
| Drag-and-drop FASTQ files for microRNA-Seq Analysis Recognition of known and prediction of novel microRNAs |
| miRspring is a software solution that creates a small portable research document that visualizes, calculates and reports on the complexities of miRNA processing. We designed an index-compression algorithm that allows the miRspring document to reproduce a complete miRNA sequence data set while retaining a small file size. Through analysis of 73 public data sets, we demonstrate miRspring's features in assessing quality parameters, miRNA cluster expression levels and miRNA processing. |
| Creates a small portable research document that visualizes, calculates and reports on the complexities of miRNA processing |
| mrSNP is a highly adaptable and performing tool for predicting the effect a 3’UTR SNP will have on miRNA binding. mrSNP predicts the impact of a SNP in a 3’UTR on miRNA binding. The proposed tool reduces the manual labor requirements and allows users to input any SNP that has been identified by any SNP-calling program. In testing the performance of mrSNP on SNPs experimentally validated to affect miRNA binding, mrSNP correctly identified 69% (11/16) of the SNPs disrupting binding. |
| Predict the impact of a SNP in a 3UTR on miRNA binding |
| ncPRO-seq is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. |
| Tool for annotation and profiling of ncRNAs using deep-sequencing data Differential expression module that allows for the multivariate analysis of samples |
| Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq data. It 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. |
| A classification module for robust biomarker detection An advanced programming interface that supports the batch submission of jobs |
| 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. |
| Including sRNA expression profiling from deep sequencing experiments Several downstream analysis tools |
| wapRNA includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data. We accept raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction. wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of gene's or miRNA's different expression in different samples. |
| Measure RNA sequence experimentally How different alleles of a gene are expressed Detect post-transcriptional mutations or identifying gene fusions Annotate the known miRNAs or predict the news |
