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Non-coding RNA identification | Small RNA sequencing data analysis

Commonly used software to identify both known and/or novel non-coding RNAs (ncRNAs) from small RNA-seq.

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omiRas
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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.
YM500
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.
miREval
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.
CPSS / Computational Platform for analysis of Small RNA deep Sequencing 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.
Oasis
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.
sRNAtoolbox
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.
DARIO
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.
NorahDesk
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.
segmentSeq
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.
PhaseTank
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.
RNASurface
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.
iSmaRT / integrative Small RNA Tool-kit
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.
miReader
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.
miR-BAG
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.
PILFER / PIrna cLuster FindER
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.
miRExpress
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.
miRA
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.).
ncRNAclassifier
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.
mirTools
Obsolete
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.
pRuNA
Obsolete
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.
moses / MOdular SEquence Suite
Obsolete
Allows to construct transparent detection workflows and to combine and compare different methods efficiently. moses integrates existing tools and methods for ncRNA detection. It processes and combines the results of different methods to find regions in a genome that contain ncRNA gene candidates. The tool provides a graphical user interface (GUI) and visualization for all intermediate steps of a workflow in order to enable the user to detect flaws in a workflow and to help to interpret the results.
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