About TetraRNADB

With the further understanding of RNA, many studies have found that some RNAs have both coding and nocoding biological functions. We developed a Tetra-classification model of RNA named TetraRNA model and used this model to analyze human RNAs, and these analyses were summarized in this database called TetraRNADB.

TetraRNADB displays the re-predicted types of human RNAs and their original types, analysis results of RNA functions etc. The database provides the dimensionally reduced bigtable of feature and the TetraRNA model. Researchers can quickly get the relevant information and results of this study from the database, and can download the required data from the database for further analysis.

Function

TetraRNADB contains five modules: Browse, Search, BLAST , Static and Download pages.

1. Browse

The BROWSE page provides some basic information: Gene ID, Transcript ID, Raw Type, Final Type, Transcript Length and ORF Length. Clicking on a Gene ID or Transcript ID will open the corresponding Ensembl page, and if you click on the Detail button, you will be redirected to the details page for that ID (containing basic information, sequence information and characterisation information). In addition, a search box is provided to quickly search for the ID you are interested in.

2. Search

Users need to select the type of data they want to query and then enter the keyword ID, which will automatically jump to the detail page after submission.

3. BLAST

You can use the BLAST tool in TetraRNADB to perform similarity sequence comparisons for genes of interest. The user needs to enter the sequence in fasta format in the search box, select the databases to be compared (mRNA, untranslated mRNA, lncRNA and translated ncRNA and all database), set the search parameters (E-value, Word size, etc.) and submit to get BLASTN results.

4. Statistic

On the static page, users can visually access statistics about the work associated with TetraRNA, including:

• Characteristic of clean datasets
• Evaluation of six models
• Feature importance of six models
• Evaluation of model prediction results
• Functional feature analysis of different human RNA classes
• The characters of peptide sequences of human tr-ncRNAs conserved in Macaca mulatta, Gorilla gorilla and Pan troglodytes
• Analysis of human and mouse homologous sequences

5. Download

On the download page we offer a range of files including Four kinds of extracted features, sequences and model files. All data is freely available to users.

Data Source

GENCODE:  https://www.gencodegenes.org/

cncRNADB:  http://www.rna-society.org/cncrnadb/