RNA Binding Site Finder

This was a quick tool I wrote for a friend. It allows the user to search a sequence of RNA for locations that could potentially bind with the search sequence. It has options to allow for partial matches where only part of the string matches a location in the RNA sequence.

Correlation with RNA Secondary Structure

By using the secondary structure configuration, it’s possible to correlate matches against locations that are single stranded. If secondary structures are added, they need to be added in a Vienna syntax. Matches are reported including the number of single stranded bases in the match.

You can try the app here.