Introduction
StructDB is a database for studying the effects of chemical modifications on the RNA secondary structure. The database collected 744,470 m6A sites across 7 species from m6A-Atlas v2.0, 135,396 RNA-editing (A-to-I) sites across 3 species, and 8,364 pseudouridine (Ψ) modification sites across 5 species from RMBase v3.0. These sites are used to measure the extent to which it affects the secondary structure of the surrounding sequence, including pre and mature RNA sequences. Two tools, ViennaRNA and RNAstructure, were applied to predict modifications, and four scores were used to quantify the structural alterations.
A user-friendly graphical interface was built to support the query, exploration, and sharing of secondary structure alteration and epitranscriptomes. This interface is annotated with putative post-transcriptional machinery, including SNP association, RBP-binding, and microRNA interaction.
User Guide
We present here StrucRMDB, A database for exploring chemical modifications affecting the secondary structure of RNA. The StrucRMDB consists of result returns from two prediction tools: RNAstructure and viennaRNA.
You need to choose one of RNAstructure and viennaRNA to see the specific content. The RNAstructure part contains m6A modification only while viennaRNA contains m6A, RNA-editing (A-TO-I), and Pseudo modification (Ψ).
1. First, make a choice between ' RNAstructure ' or viennaRNA ' and specify the modification type.
2. Overview of queried data.
This page displays the results under the conditions that you just selected. Pie charts show the percentage of gene region and RNA type. You may also change the condition of this interface.
Detailed information is listed in the table, containing the basic site information, modification type, gene name, gene region, gene type, four types of scores, as well as involved RNA binding proteins, miRNA target,and SNP.
You can click "ID" to see more information.
Parameter description
StructRM ID: Unique datatbase ID identification
Modification: types of modifications
Species: types of species
Chromosome: Chromosome name
Position: modification coordinate
Gene: List of genes where RNA modification sites are located
Gene Region: Genetic characteristics of RNA modification site distribution
Gene Type: Genetype of RNA modification site distribution
Classification: Classification based on relative score, RNA Distance, and SMC score
Similarity Score: a score comparing RNA secondary structures returned by RNAforester
Relative score: relative score returned by RNAforester, calculated using Similarity Score.
RNA Distance: calculated distance instead of similarity score returned by RNAforester
SMC score: a type of Score used to quantify similarity between RNA secondary structure returned by RNAsmc
RBP: RNA binding protein number associated with modification site
miRNA： microRNA number associated with modification site
SNP： Single Nucleotide Polymorphism number associated with modification site
3. Overview of modification sites.
This page includes more detailed information including the primary sequence, secondary structure (dot-bracket file), and visualization. You can click the plot to see a amplified picture.
Download
1. Click 'Download' to obtain the data.
2. Click the blue 'CSV' button to download the data from structRMDB.
API
1. Click 'API' to view and obtain the data.
2. It's an application program interface. This set of APIs was made to let our users reach the information they wanted in a new pragmatical way. Click the URL link to view the example.
