RNA Analyzer³

About

With the increase in transcriptomic data, sequence analysis is getting more complex and requires a variety of tools to understand the function of a given sequence. To overcome this, we present RNA Analyzer³ (https://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/), which can be used to give an overview of user-provided RNA sequence(s).

We created this tool with a focus on giving a rundown of the regulatory features present in any given sequence. RNA Analyzer³ has built-in several motif searches, including Rfam, which can identify regulatory motifs in a given sequence. RN Analyzer also incorporates RNAfold from the ViennaRNA package to give the user structural information along with a folding overview. These, coupled with coding sequence potential analyis, can help annotate the nature of the sequence which can be regulatory or protein coding. We achieve this using specific/well-known databases and tools built for specific predictions, all coupled in one web application. Furthermore, we also allow users to predict microRNA target predictions present in the given sequence, which can be useful in understanding gene regulation.

Apart from these, RN Analyzer³ also has tRNA scan, iron responsive element (IRE) identification, UTR prediction, small molecule binding site identification, and can also scan for highly structured regions which are usually involved in regulatory functions.

For more information about the working of RN Analyzer, please check our publication:

A helpful guide is also present for users on how to use and check results.

Help

Structural Information:

Several structural features like stems, loops, stem gg pairs are calculated using ViennaRNA tools which is also used to create the folding and then FORNA is used for annotation and interactive visualization.

Motif Scans:

• Trans-Splicing: Trans-splicing involves the RNA splicing of separate precursors giving rise to one mature mRNA. More information about this can be found here.
• IRE: Iron-responsive elements in RNA are binding sites for iron-regulatory protein. More infomation about IRE can be found here.
• ARE: AU-rich regions in RNA are sequences with a high proportion of adenine (A) and uracil (U) nucleotides that often regulate mRNA stability and translation.
• SMsite: SM site (splicing motif site) is a short RNA sequence that serves as a recognition signal for the splicing machinery during pre-mRNA processing.
• RNA Motif: RNA motif is a sequence or structural pattern in RNA that plays a specific biological role, such as binding proteins, guiding RNA folding, or regulating processes like splicing, translation, or stability. We use Rfam database of RNA motifs combined with infernal for scanning user sequence(s).
• Protein Binding Motifs: RBP motifs are RNA sequence that RNA-binding proteins recognize and bind to in order to regulate RNA.
• CstF Binding Motifs: CstF binds GU-rich RNA to promote pre-mRNA cleavage and polyadenylation.

Folding Options:

• MFE: Predicts the minimum free energy structure of your RNA sequence using RNAfold. This is the default option.
• Centroid: Predicts the centroid structure, which is the structure with the minimum average base-pair distance to all other structures in the ensemble.
• Pseudoknots: Detects pseudoknot structures using IPknot in your RNA sequence. Pseudoknot prediction is for visualization purposes only as other motif scans require MFE calculations and is limited to 2500nt due to longer run times with optimal thresholds from the IpKnot article.
• Suboptimal structures: Predicts suboptimal structures using RNAsubopt from ViennaRNA. Due to exponential run times, this option is limited to max 1500 nucleotides per run.

Visualization options:

• Draw Annotated Structure: Option to generate the annotated RNA structure caulcauted by RNAfold with highlighted motifs predicted by RNA Analyzer³. Users can choose between VARNA or FORNA for the visualization. In VARNA annotations, some artifacts can be expected due to unnatural connections within the RNA strcuture. If this is the case for a particular sequence, users can opt for the FORNA visualization instead.

RNA type scanning

• tRNA scan: Detects and annotates transfer RNAs (tRNA) in the given sequence using tRNAscan-SE.
• miRNA scan: Finds potential miRNA sequences in the given sequence using miRBase database with nhmmer from hmmer.

Coding Annotation:

• Coding Potential: Coding potential of the given sequnece is calculated using CPC2 package and is defualt behaviour.
  However users can also chose augustus for some model species for a indepth gene prediction.
• UTR prediction: If augustus does not predict UTRs, then the prediction is simply taken from coding sequence boundries. To further make the UTR scanning more biological relevent, the sequnce is also checked for polyA signals and then use it to interprt the 3' UTR.

miRNA target prediction:

• Scans the sequence to find targets for known miRNA(s) from the miRBase database using a custom python wrapper over Miranda. If 3' Utr is predicted then uses the 3' UTR sequence for scanning making it more biological relevent.