Curator Dashboard

Data set of 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.

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• SciCrunch
• 13 years ago - by Anonymous

An online database for miRNA target prediction and functional annotations.

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• SciCrunch
• 13 years ago - by Anonymous

Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data.

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• SciCrunch
• 13 years ago - by Anonymous

Database of computationally predicted targets for microRNAs across many species.

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• SciCrunch
• 13 years ago - by Anonymous

Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.

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• SciCrunch
• 13 years ago - by Anonymous

A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Database serving as a tool for microRNA target prediction. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behaviour of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTARdb contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets. There are two ways to interrogate HOCTARdb: (i) by selecting a miRNA using either an alphabetically sorted pull-down menu in the microRNA query, or (ii) by typing a target gene symbol (HUGO Gene Name-approved) in the Target Gene Name query.

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• SciCrunch
• 13 years ago - by Anonymous

Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions.

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• SciCrunch
• 13 years ago - by Anonymous

Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.

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• SciCrunch
• 13 years ago - by Anonymous

A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded.

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• SciCrunch
• 13 years ago - by Anonymous

Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.

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• SciCrunch
• 13 years ago - by Anonymous

Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.

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• SciCrunch
• 17 years ago - submitted by Eddy Kim

A software 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. ShortStack discovers small RNA ''clusters'' de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes, and other Hairpin-associated small RNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, a table describing the results of the hairpin / MIRNA analysis for each cluster, and detailed text-based alignments of all MIRNAs and hairpin-associated clusters. It can also be run in ''count'' mode, to quantify a set of input loci with genomic coordinates determined a priori by the user. ShortStack is a perl program. Besides perl, ShortStack also requires samtools and the RNALfold and RNAeval programs from the Vienna RNA Package to execute. When used to control the alignment of small RNA data to a reference genome, ShortStack also requires bowtie and bowtie-build. Finally, for optimal results, ShortStack uses a file of inverted repeats produced by the EMBOSS application einverted.

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• SciCrunch
• 13 years ago - by Anonymous

A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.

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• SciCrunch
• 13 years ago - by Anonymous

Pipeline scripts for creating a miRspring (miRNA sequence profiling) document, a new way of sharing and analysing sequencing data for small RNA.

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• SciCrunch
• 13 years ago - by Anonymous

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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• SciCrunch
• 13 years ago - by Anonymous

A web tool for simple microRNA prediction in genome sequences.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous