1 |
BioVLAB-MMIA-NGS |
BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. |
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human mice macaca plants (rice) |
seed matchconservationfree energysite accessibilitytarget-site abundance3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
Sept. 29, 2014
Citations: 8
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2 |
CleaveLand4 |
CleaveLand a generalizable computational pipeline for the detection of cleaved miRNA targets from degradome data. CleaveLand takes as input degradome sequences, small RNAs and an mRNA database and outputs small RNA targets. |
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any |
seed matchconservationfree energyG:U pairs allowed in the seeddegradome seq analysis |
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Homepage
Publication
Nov. 18, 2008
Citations: 312
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3 |
ComiR |
ComiR (Combinatorial miRNA targeting) predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. |
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human mouse worm fly |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU contentmiRNA expression level |
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Homepage
Publication
Dec. 20, 2012
Citations: 22
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4 |
comTAR |
comTAR allows users to analyze the variations of known miRNA targets during evolution and to predict previously unknown interactions by focusing on the conservation of the potential targeting. |
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plants |
seed matchconservationfree energyG:U pairs allowed in the seed |
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Homepage
Publication
March 14, 2014
Citations: 5
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5 |
CPSS |
CPSS is (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. |
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human mouse rat chicken fish other animals (selectable) |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
May 9, 2012
Citations: 25
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6 |
DeAnnIso |
DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. |
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human mouse fish fly plants (selectable) |
seed matchconservationfree energytarget-site abundance3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
May 13, 2016
Citations: 20
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7 |
DIANA-microT-CDS |
DIANA-microT-CDS is the 5th version of the microT algorithm. It is specifically trained on a positive and a negative set of miRNA Recognition Elements (MREs) located in both the 3'-UTR and CDS regions. DIANA-microT-CDS provides a significant increase in sensitivity compared to the previous version (65% vs 52%), when compared against experimental proteomics data. |
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human mouse fly worm |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
May 16, 2013
Citations: 613
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8 |
ElMMo3 |
A Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and assigns a posterior probability to each putative target site. |
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human mouse rat fish fly worm |
seed matchconservationG:U pairs allowed in the seedBayesian method |
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Homepage
Publication
March 1, 2007
Citations: 176
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9 |
GUUGle |
GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length. |
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any |
seed matchG:U pairs allowed in the seed |
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Homepage
Publication
Jan. 10, 2006
Citations: 23
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10 |
IntaRNA |
IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. |
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any |
seed matchfree energysite accessibilitytarget-site abundanceG:U pairs allowed in the seed |
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Homepage
Publication
Oct. 21, 2008
Citations: 260
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11 |
isomiR2Function |
somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. |
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plants |
seed matchconservationfree energyG:U pairs allowed in the seeddegradome seq analysis |
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Homepage
Publication
March 21, 2017
Citations: 10
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12 |
LeARN/smallA |
A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. |
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any |
seed matchconservationfree energyG:U pairs allowed in the seed |
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Homepage
Publication
Jan. 14, 2008
Citations: 8
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13 |
MicroTar |
MicroTar is a microRNA target prediction program based on mRNA sequence complementarity (3'-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA molecules. It uses the RNAlib library from the Vienna RNA package |
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animals |
seed matchfree energysite accessibilityG:U pairs allowed in the seed |
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Homepage
Publication
Dec. 18, 2006
Citations: 44
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14 |
miRabel |
miRabel is a efficient tool for the prediction of miRNA target mRNAs and their associated biological functions.
miRabel aggregated all human results of four important prediction algorithms (miRanda, PITA, SVmicrO, and TargetScan) showing additional characteristics in order to rerank them into a single list. |
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human |
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Homepage
Publication
Jan. 28, 2020
Citations: 51
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15 |
miRanda |
miRanda algorithm is based on a comparisone of miRNAs complementarity to 3'UTR regions. The binding energy of the duplex structure, evolutionary conservation of the whole target site and its position within 3”UTR are calculated and account for a final result which is a weighted soum of match and mismatch scores for base pairs and gap penalties. |
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any |
seed matchconservationfree energyG:U pairs allowed in the seed |
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Homepage
Publication
Oct. 5, 2004
Citations: 1807
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16 |
miRcode |
Provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation, including >10,000 long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. Site conservation is evaluated based on 46 vertebrate species. |
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human |
seed matchconservation |
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Homepage
Publication
June 19, 2012
Citations: 419
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17 |
miRDB |
Recently updated features of miRDB, includes 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest. |
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human mouse rat dog chicken |
seed matchconservationfree energysite accessibilitymachine learning3' compensatory pairinglocal AU content |
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Homepage
Publication
Nov. 5, 2014
Citations: 1006
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18 |
miRmap |
To evaluate the strenght of the resulting mRNA repression, the miRNA taregt predictors may employ thermodynamic, evolutionary, probabilistic, or sequence-based features. An open source software library, miRmap, for the first time comprehensively covers all four approaches using eleven predictor features, three of which are novel. Overall, target site accessibility appears to be the most predictive feature. Moreover novel feature based on PhyloP, which evaluates the significance of negative selection, is the best performing predictor in the evolutionary category. |
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human mouse rat cow chicken zebrafish other animals (selectable) |
seed matchconservationfree energysite accessibilitylocal AU contentSite over-representation probability |
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Homepage
Publication
May 28, 2013
Citations: 72
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19 |
miRTar2GO |
miRTar2GO is a method that predicts miRNA targets by allocating CLIPed regions of the mRNA 3' UTRs to miRNA seed regions. |
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human |
seed matchsite accessibilitymRNA differential expression |
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Homepage
Publication
April 7, 2017
Citations: 4
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20 |
mirTools 2.0 |
MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. |
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human mouse rat chicken fish worm fly other animals (selectable) plants (selectable) any (local) |
seed matchconservationfree energysite accessibilitymachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
May 29, 2013
Citations: 40
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21 |
MIRZA-G |
A suite of algorithms for the prediction of miRNA targets and siRNA off-targets on a genome-wide scale. The MIRZA-G variant that uses evolutionary conservation performs better than currently available methods in predicting canonical miRNA target sites and in addition, it predicts non-canonical miRNA target sites with similarly high accuracy. Furthermore, MIRZA-G variants predict siRNA off-target sites with an accuracy unmatched by currently available programs. |
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human |
seed matchconservationfree energysite accessibility3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
Jan. 27, 2015
Citations: 31
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22 |
MRmicroT |
MR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences. |
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mousehuman |
seed matchconservationfree energysite accessibilityG:U pairs allowed in the seed |
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Homepage
Publication
June 30, 2014
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23 |
MTide |
MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. |
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plants |
seed matchconservationfree energy3' compensatory pairingG:U pairs allowed in the seeddegradome seq analysis |
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Homepage
Publication
Sept. 24, 2014
Citations: 41
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24 |
MultiMiTar |
MultiMiTar is a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. |
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human |
seed matchsite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU contentArchived Multi-Objective Simulated Annealing |
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Homepage
Publication
Sept. 15, 2011
Citations: 19
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25 |
Oasis 2.0 |
Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (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 advanced programming interface 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. |
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human mouse fly fish worm chicken rat other animals (selectable) |
seed matchconservationfree energyG:U pairs allowed in the seed |
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Homepage
Publication
Feb. 19, 2015
Citations: 33
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26 |
P-TAREF |
p-TAREF refines the process of microRNA target identification through incorporation of local interaction information for microRNA and target region in the target sequence as well as estimates the candidature of being a true microRNA target on the basis of intrinsic sequence property around the target site determined by varying dinculeotide density profile. Also by considering dinculeotide density we incorporate the nearest neighbor approach of RNA structure determination. |
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plants |
seed matchconservationfree energytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
Dec. 29, 2011
Citations: 17
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27 |
PicTar |
PicTar is a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published microRNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. |
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vertebrates fly worm |
seed matchconservationfree energytarget-site abundanceHMM |
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Homepage
Publication
April 3, 2005
Citations: 2220
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28 |
PITA |
PITA offers a brand new view on the miRNA target prediction. The main assumption is based on the fact the mRNA structure plays a role in target recognition by thermodynamically promoting or disfavoring the interaction. |
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human (online) fly (online) mouse (online) worm (online) animals (local) |
seed matchfree energysite accessibilitytarget-site abundanceG:U pairs allowed in the seed |
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Homepage
Publication
Sept. 23, 2007
Citations: 1252
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29 |
psRNATarget |
psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. |
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plants |
seed matchsite accessibilitytarget-site abundanceit distinguishes translational and post-transcriptional inhibition |
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Homepage
Publication
May 27, 2011
Citations: 784
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30 |
psRobot |
psRobot is designed to analyze batch of plant small RNA data.The online version of psRobot has two modules. The stem-loop small RNA prediction module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences. The second one, small RNA target prediction module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants. |
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plants |
seed matchconservationtarget-site abundance3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
June 12, 2012
Citations: 245
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31 |
RNA22 |
Rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not relay upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. |
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animals |
seed matchfree energyG:U pairs allowed in the seedsensitivity/specificity settingspattern recognision |
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Homepage
Publication
July 26, 2006
Citations: 992
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32 |
RNAhybrid |
RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. |
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any |
seed matchfree energytarget-site abundance3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
July 1, 2006
Citations: 902
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33 |
sPARTA |
A powerful tool for plant miRNA target prediction and PARE validation. It can search for targets in unannotated genomic regions, which is useful to discover novel regulatory modules, independent of genome annotations that may be incomplete. |
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plants |
seed matchtarget-site abundanceG:U pairs allowed in the seeddegradome seq analysis |
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Homepage
Publication
Aug. 12, 2014
Citations: 36
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34 |
sRNAtoolbox |
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. |
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human mouse rat chicken fly fish viruses plants (selectable) bacteria other animals (selectable) |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
May 27, 2015
Citations: 118
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35 |
sRNAtools |
sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes. |
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plantsanimalsmousefishwormratflyhuman |
seed matchconservationfree energyG:U pairs allowed in the seed |
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Homepage
Publication
Jan. 18, 2021
Citations: 21
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36 |
STarMir |
STarMir is a tool for predicting potential binding sites for one or multiple microRNAs (miRNA) in a target RNA sequence (typically mRNA). It is based on the logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies. Each of the candidate sites is assigned a logistic probability as a measure of confidence in the predicted site. |
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any |
seed matchfree energysite accessibility3' compensatory pairingG:U pairs allowed in the seedlocal AU contentCLIP-based |
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Homepage
Publication
May 6, 2014
Citations: 51
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37 |
submiRine |
An open-source software package for predicting microRNA target site variants (miR-TSVs) from clinical genomic data sets that measure miRNA expression, gene expression, and genotype. The main benefits of SubmiRine are that it allows for de novo prediction of miR-TSVs from custom data sets - such as those that can be generated from large-scale clinical genomics projects - and provides a methodology to prioritize predicted miR-TSVs by their relative probability of being functional. |
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human |
seed matchconservationsite accessibilitytarget-site abundance3' compensatory pairinglocal AU content |
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Homepage
Publication
March 26, 2015
Citations: 9
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38 |
SVMicrO |
SVMicrO is mammalian miRNA target prediction algorithm, which assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SMVicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by training from a comprehensive collection of 113 site and 30 UTR features. Comprehensive evaluation of SVMicrO performance has been carried out on the training data, proteomics data, and immunoprecipitation (IP) pull-down data. |
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mammals |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
Sept. 22, 2010
Citations: 45
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39 |
TaLasso |
TaLasso algorithm combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets. |
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human |
seed matchconservationfree energysite accessibilitytarget-site abundance3' compensatory pairingG:U pairs allowed in the seedlocal AU contentmiRNA & mRNA expression (needed)HMM |
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Homepage
Publication
Feb. 14, 2012
Citations: 38
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40 |
TAPIR |
TAPIR is designed for the prediction of plant microRNA targets. This web server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. |
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plants |
seed matchfree energy3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
April 28, 2010
Citations: 145
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41 |
Target-align |
A Smith-Waterman-like alignment tool was developed in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace the optimal local alignments. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings. |
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plants |
seed match3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
Oct. 7, 2010
Citations: 31
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42 |
TargetMiner |
A robust tool for microRNA target prediction with systematic identification of negative examples. TargetMiner is a support vector machine (SVM)-based classifier. |
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human |
seed matchconservationfree energysite accessibilitytarget-site abundancemachine learning3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
Aug. 19, 2009
Citations: 103
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43 |
TargetRank |
TargetRank scores the seed matches in a UTR relative to a given siRNA or miRNA, and then calculates an overall score for the mRNA as a whole by summing the scores for all seed matches present in the 3' UTR. |
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human mouse |
seed matchconservationtarget-site abundancelocal AU content |
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Homepage
Publication
Sept. 5, 2007
Citations: 194
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44 |
TargetRNA2 |
TargetRNA2 is a web server that identifies mRNA targets of sRNA regulatory action in bacteria. As input, TargetRNA2 takes the sequence of an sRNA and the name of a sequenced bacterial replicon. When searching for targets of RNA regulation, TargetRNA2 uses a variety of features, including conservation of the sRNA in other bacteria, the secondary structure of the sRNA, the secondary structure of each candidate mRNA target and the hybridization energy between the sRNA and each candidate mRNA target. |
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bacteria |
seed matchconservationfree energysite accessibility3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
April 21, 2014
Citations: 93
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45 |
TargetScan |
TargetScan predicts biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each miRNA. As an option, only conserved sites are predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing and centered sites. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using cumulative weighted context++ scores of the sites. As an option, predictions are also ranked by their probability of conserved targeting. TargetScanHuman considers matches to human 3' UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within open reading frames (ORFs). Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context++ model), uses 3' UTR profiles that indicate the fraction of mRNA containing each site, and uses updated miRNA families. |
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human mouse fly worm fish |
seed matchconservationfree energysite accessibilitytarget-site abundance3' compensatory pairingG:U pairs allowed in the seedlocal AU content |
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Homepage
Publication
Aug. 12, 2015
Citations: 3868
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46 |
TargetSpy |
TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. It does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. |
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human mouse chicken rat fly |
free energysite accessibilitymachine learning3' compensatory pairing |
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Homepage
Publication
May 28, 2010
Citations: 76
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47 |
TarPmiR |
Approach for miRNA target site prediction which includes 13 different features. |
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human |
seed matchconservationfree energysite accessibilitymachine learning3' compensatory pairinglocal AU contentm/e motif the total number of paired positions the length of the target mRNA region the lenght of the largest consecutive pairings and two others |
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Homepage
Publication
May 20, 2016
Citations: 83
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48 |
UEA sRNA 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. |
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plants animals viruses |
seed match3' compensatory pairingG:U pairs allowed in the seedRule-Based Complementarity Search degradome seq analysis |
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Homepage
Publication
May 24, 2012
Citations: 149
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49 |
wapRNA |
wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on. |
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human mouse rat worm fly chicken worm fish other animals (selectable) any (local) |
seed matchconservationfree energytarget-site abundance3' compensatory pairingG:U pairs allowed in the seed |
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Homepage
Publication
Sept. 6, 2011
Citations: 26
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50 |
WMD3 |
WMD3 - Web app for the automated design of artificial plant microRNAs. Platform requires only selection of favorite candidates according to a small set of criteria. It is designed to optimize both intrinsic small RNA properties as well as specificity within the given transcriptome. |
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plants |
seed matchfree energysite accessibility |
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Homepage
Publication
Feb. 4, 2008
Citations: 236
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