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StarScan is developed for scanning small RNA (miRNA, piRNA, siRNA) mediated RNA cleavage events in lncRNA, circRNA, mRNA and pseudo genes from degradome sequencing data. web-based software: website [4] Cupid: Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA ...
MicroRNA sequencing (miRNA-seq), a type of RNA-Seq, is the use of next-generation sequencing or massively parallel high-throughput DNA sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is often enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and ...
Databases can be used to pair mRNA- and miRNA-data that predict miRNA-targets based on their base sequence. [150] [151] While this is usually done after miRNAs of interest have been detected (e. g. because of high expression levels), ideas for analysis tools that integrate mRNA- and miRNA-expression information have been proposed. [152] [153]
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
It is recommended to name the SVG file “Miran-seq-library-prep.svg”—then the template Vector version available (or Vva) does not need the new image name parameter. Licensing The copyright holder of this file allows anyone to use it for any purpose, provided that the copyright holder is properly attributed.
The quantity of RNA present is inferred from the probe signal’s intensity. While Northern Blotting is highly specific and helpful for validating high-throughput methods like RNA-seq, it requires a large sample volume, is time-consuming, and lacks precision in quantification analysis. [10] [11]
SpliceR An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. SpliceSEQ SpliceViewer is a Java application that allows researchers to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that ...
CLIPSim-MC: CLIPSim-MC is a tool that uses CLIP-seq data to find miRNA/MRE pairings using a Monte-Carlo-based approach. [1]starBase database: a database for exploring miRNA-mRNA, miRNA-lncRNA, miRNA-sncRNA, miRNA-circRNA, miRNA-pseudogene, protein-lncRNA, protein-RNA interactions and ceRNA networks from HITS-CLIP (CLIP-Seq, PAR-CLIP, iCLIP, CLASH) data, and TargetScan [2], PicTar, RNA22 ...