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ncRNA identification (small RNA-seq analysis)

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

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omiRas
Web

omiRas

A Web service for the analysis of ncRNA datasets derived from Illumina sRNA-Seq…

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…

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miRDeep
Desktop

miRDeep

miRDeep is a completely overhauled tool which discovers microRNA genes by…

miRDeep is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.

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miRDeep-P
Desktop

miRDeep-P

A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

A computational tool for analyzing the microRNA (miRNA) transcriptome in plants.

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YM500
Web

YM500

Provides small RNA (smRNA) sequencing in human cancer research. YM500 not only…

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),…

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miREval
Web

miREval

An online tool that can simultaneously search up to 100 sequences for novel…

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…

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miRDeep*
Desktop

miRDeep*

An integrated application tool for miRNA identification from RNA sequencing…

An integrated application tool for miRNA identification from RNA sequencing data.

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segmentSeq
Desktop

segmentSeq

Analyses small RNA sequencing data from multiple biological sources, taking…

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…

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MIReNA
Desktop

MIReNA

A tool to find microRNAs with high accuracy and no learning at genome scale and…

A tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

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pssRNAMiner
Web

pssRNAMiner

Identifies phased small RNA clusters as ta-siRNA candidates by evaluating the…

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…

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PhaseTank
Desktop

PhaseTank

A stand-alone package for systematically characterizing phasiRNAs and their…

A stand-alone package for systematically characterizing phasiRNAs and their regulatory networks. PhaseTank can identify phasiRNAs/tasiRNAs functional cascades (miRNA/phasiRNA --> PHAS loci -->…

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miRspring
Desktop

miRspring

Allows to share and analyze aligned small RNA sequencing data. miRspring is a…

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…

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CoRAL
Desktop

CoRAL Classification of RNAs by Analysis of Length

A machine learning package that can predict the precursor class of small RNAs…

A machine learning package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset.

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miRExpress
Desktop

miRExpress

A stand-alone software package implemented for generating miRNA expression…

A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.

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ShortStack
Desktop

ShortStack

A tool developed to process and analyze small RNA-seq data with respect to a…

A tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

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iSmaRT
Desktop

iSmaRT integrative Small RNA Tool-kit

Analyzes smallRNA-Seq data. iSmaRT is a collection of bioinformatics tools and…

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…

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isomiR-SEA
Desktop

isomiR-SEA isomiR Seed Extension Aligner

Produces accurate miRNAs expression level quantification and both isomiRs and…

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…

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miRPlant
Desktop

miRPlant

An integrated package for identification of plant miRNA from RNA sequencing…

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…

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RNAspace.org
Web
Desktop

RNAspace.org

Allows to create web sites dedicated to non-protein-coding RNA (ncRNA)…

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…

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NorahDesk
Desktop

NorahDesk

A small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq)…

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…

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miR-PREFeR
Desktop

miR-PREFeR miRNA PREdiction From small RNA-Seq data

Utilizes expression patterns of miRNA and follows the criteria for plant…

Utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

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miRA
Desktop

miRA

A tool to identify miRNA precursors in plants, allowing for heterogeneous and…

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…

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miRSeqNovel
Desktop

miRSeqNovel

An R/Bioconductor based workflow for novel miRNA prediction from deep…

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

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Find-miRNA
Desktop

Find-miRNA

Finds pre-miRNAs in a RNA sequence and miRNA in each found pre-miRNA. FindMiRNA…

Finds pre-miRNAs in a RNA sequence and miRNA in each found pre-miRNA. FindMiRNA analyzes the users sequences with the sliding window of 100nt. It then uses another program to calculate the optimal…

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miRCat
Desktop

miRCat miRNA Categorisation

Predicts miRNA on both plant and animal data. miRCat is a part of the UEA small…

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…

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SeqCluster
Desktop

SeqCluster

A framework python for the annotation and classification of the non-miRNA small…

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…

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deepBlockAlign
Desktop

deepBlockAlign

Introduces a two-step approach to align RNA-seq read patterns with the aim of…

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…

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piClust
Web

piClust

Finds piRNA clusters and transcripts from small RNA-seq data. piClust uses a…

Finds piRNA clusters and transcripts from small RNA-seq data. piClust uses a density based clustering approach without assumption of any parametric distribution.

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miReader
Desktop

miReader

Detects mature miRNAs directly from next generation sequencing read data,…

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…

miR-BAG
Web
Desktop

miR-BAG

Identifies miRNA candidates with high accuracy and stable performance over wide…

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…

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RNASurface
Desktop

RNASurface

Reconstructs the surface of structural potential using an algorithm for Z-score…

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…

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proTRAC
Desktop

proTRAC probabilistic TRacking and Analysis of Clusters

A software which detects and analyses piRNA clusters based on quantifiable…

A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.

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pRuNA
Web

pRuNA

Identifies all potential regulatory ncRNAs that can establish stable joint…

Identifies all potential regulatory ncRNAs that can establish stable joint structures with a query mRNA. pRuNA provides a sequence filter which eliminates a significant fraction of the available…

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smyRNA
Desktop

smyRNA

Exploits differential distribution of k-mer motifs among ncRNAs with respect to…

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…

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MirPlex
Desktop

MirPlex

A tool for miRNA prediction that requires only sRNA datasets as input. Mature…

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…

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MIREAP
Desktop

MIREAP

A tool which can be used to identify both known and novel microRNAs from small…

A tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

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miRTRAP
Desktop

miRTRAP miRNA Tests for Read Analysis and Prediction

Incorporates the mechanisms of miR biogenesis and includes additional criteria…

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…

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moses
Desktop

moses MOdular SEquence Suite

Allows to construct transparent detection workflows and to combine and compare…

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…

mirExplorer
Desktop

mirExplorer

A prediction tool which is based on an integrated adaptive boosting method and…

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,…

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MiRAuto
Desktop
Web

MiRAuto

A fully automated user-friendly tool for predicting miRNAs from small RNA…

A fully automated user-friendly tool for predicting miRNAs from small RNA sequencing data in both model and non-model plant species. miRAuto enables users to identify miRNAs in non-model plant…

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