About OPP_ncRBase

OPP_ncRBase(ncRNA database for oil producing plants) collected miRNAs, lncRNAs and circRNAs for oil producing plants. In additions to existing annotations for oil producing plants, we predicted many miRNAs, lncRNAs and circRNAs from high-throughput sequencing data using the following pipelines.

Pipeline of miRNA prediction

We use miRNA seq data from SRA(Sequence Read Archive) to prediction miRNAs for oil plants with genome. And for oil plants which haven’t genome, we use RNA seq data or EST data to prediction their miRNAs.

Pipeline of lncRNA prediction

We use RNA seq data from SRA to prediction lncRNAs for oil plants.

Pipeline of circRNA prediction

We used software PcircRNA_finder to prediction circRNAs for oil plants. The figure is flowchart of PcircRNA_finder for circRNA prediction. It consists of three modules.

Browse

The browsing facility allows a user to explore the data for ncRNAs by species.

Search

ID Search

A ID search feature allows users to search the database with keywords such as ncRNA accession, name or keywords.

Tissue

Tissue feature allows users to search the RNA seq libraries we used to predict ncRNAs.

Genomic Location

Tissue feature allows users to search ncRNAs according to their genomic location.

Batch Search

Batch Search feature allows users to search a lot of ncRNAs one time.

By Sequence

By Sequence feature allows users to search database by sequences.

New microRNA Prediction

New microRNA Prediction tool allows users to predict miRNAs using their own deep sequencing data.

Blast

Blast can help users to find similar sequences against their input sequences.

Downloads

We provide all sequences of our entries for users.