Convert ct file to dot bracket format

Question

[abdullahrenk]

Is there a program that can convert ct files to dot bracket format? I have RNA structures in ct format and would like to extract secondary structure information from it. ie which nucleotide are participating in the formation of stem loops, hair pins, multi-loops, psuedoknots etc. Forgi is a program that can do this but it only takes dot bracket files as input.

Answer 1

[ricovox]

There are plenty of programs that can convert between dot-bracket notation and CT format.

You can use the program dot2ct. It is part of the RNAstructure package written by the Mathews Lab at the University of Rochester. You can download RNAstructure here.

Or you can use their free online webserver. The dot2ct tool is here.

The RNAstructure package (the webservers OR the downloadable package) can also predict RNA secondary structures and alignments.