tRF target predictions limited to 50k entries

[kaikummer]

hi, is there a way to get all predicted target sites per tRF via the web tool? only the first 50K are displayed (targets are shown when searched via genes, as those are less than 50K).
best, kai

[az7jh2]

Hi Kai,

Thank you for your interest in tRFtarget.

At present, tRFtarget allows access to the top 50,000 binding sites in a single search. These sites are selected based on their lower free energy and larger maximum complementary length. Unfortunately, it isn't possible to display all binding sites on our webpage due to the increased data transmission time, resulting a significant increase in waiting times for users.

To give you some context, if you were to search for a binding site for a single human tRF, our database (which includes over 530,000 indexed target RNAs) indexes an average of 2 to 3 binding sites per target RNA. This results in more than one million binding sites predicted by RNAhybrid and another million predicted by IntaRNA. Consequently, displaying all these binding sites in a web page is simply not feasible.

However, there is an alternative if you need access to all predicted binding sites for a specific tRF. You can run the tRFtarget-pipeline locally or utilize our online service for the specific tRF and all target RNAs of interest.

I am sorry for the inconvenience. By the way, do you think a new feature to download all searched binding sites might be helpful?

[kaikummer]

Hi Ningshan,
thank you very much for your fast reply! I will definitely try the tRFtarget-pipeline!
Re your question: i mean, the export to .csv is anyways more or less a download of all searched binding sites (at least the displayed one), but maybe this could allow the complete download of more than the 50K binding sites without major issues with displaying them in the web page?
Again thank you very much!
Best, Kai

[az7jh2]

Hi Kai,

The export button on top of the table displaying retrieved binding sites is designed to export just the table to csv file. But we can add a new feature to allow users to download all retrieved binding sites without displaying it. We will start to work on it and implement this new feature in the next update of tRFtarget.

I will keep you posted when the new version with this new feature is available.

Ningshan

[az7jh2]

Hi Kai,

Apologies for the very long delay in responding. During the update and maintenance of tRFtarget, we decided NOT to include a feature for downloading all retrieved binding sites. The reasons are as follows:

1. Predicted binding sites with lower quality scores are ranked at the end and have a high false discovery rate. Therefore, we strongly recommend focusing on high-confidence binding sites, characterized by lower free energy and greater maximum complementary length.
2. Our database includes millions of target RNAs, and for each tRF-RNA pair we store up to five predicted binding sites. As a result, the indexed binding site records are extremely large. Downloading all results for a single query is not feasible within typical time limits and would also impose substantial load on our backend.

Therefore, we have decided NOT to implement this feature. If you still want to access to all predicted binding sites, as previously recommended, you can run the tRFtarget pipeline locally or use our online service for specific tRFs and their target RNAs of interest.

I will close this issue for now. Please feel free to reach out if you have any further questions.

Thank you again for your interest in tRFtarget.