Next Generation Sequencing Applicationsspecialized


These applications are designed for the analysis of smallRNA-seq data from next generation sequencing experiments. Some of them have a Web interface but others need local installation.



Web / Local installation


UEA SmallRNA workbench

The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. NO / YES PMID: 28439835


A system for MicroRNA-MRNA Integrated Analysis using High throughput Sequencing data by Utilizing Cloud Computing Environment. YES / NO PMID: 25270639


A suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism. Additionally, it enables differential expression, miRNA-mRNA target prediction and/or functional analysis. It requires a local installation. NO / YES PMID: 27167008


A complete web tool for the analysis, quantification and differential expression of small RNAs in biological samples from NGS data. NO / YES PMID: 26019179

Oasis 2.0

Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-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. YES / NO PMID: 25701573


Classification of the large-scale short reads into known categories, such as known miRNAs, non-coding RNA, genomic repeats or coding sequences. Discovery of the novel miRNAs from the high-throughput sequencing technology.Identification of the differentially expressed miRNAs according to read tag counts (the number of reads for each tag reflects relative express level). YES / NO PMID: 23778453


The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, …). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data NO / YES PMID: 23221645


A novel database, developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. YES / NO PMID: 26590255


A systematic method, for extracting miRNA expression profiles from sequencing reads generated by second-generation sequencing. miRExpress contains miRNA information from miRBase and efficiently reveals miRNA expression profiles by aligning sequencing reads against the sequences of known miRNAs. miRExpress can be used to find novel miRNA candidates by aligning reads with sequences of known miRNAs of various species. NO / YES PMID: 19821977


AltAnalyze is an easy-to-use application for the end-to-end analysis of microarry, single-cell and bulk RNA-Seq data. AltAnalyze can assess gene expression along protein isoforms, domain composition and microRNA targeting. NO / YES PMID: 20513647


miRCat is a tool to identify miRNAs in high-throughput small RNA sequence data. miRCat takes a FASTA file of small RNA reads as input and will map them to a reference genome. The tool then looks at genomic hit distribution patterns and secondary structure of genomic regions corresponding to sRNA hits and will predict miRNAs and their precursor structures. miRCat has been tested on published datasets. It is part of the SmallRNA workbench NO / YES PMID: 28407097