Welcome to rna_align package

This is a web-based gateway that allows you to remotely run our software on our server. To continue, simply fill in the requisite data below. Example input data for the software may be found here. This program computes the alignment between two RNA structures.

There are three sections to the data: first, the name of the RNA and the primary structure of the RNA (see the example data file for formatting), followed by the secondary structure of the RNA, followed by the tertiary structure of the RNA. Each section is separated by the '>' character alone on a line. If there is no tertiary structure, then after the '>' that ends secondary structure section, there should be another '>' in the next line.

The secondary and tertiary structures of the RNA are specified as follows:

(<stem number>)    <start base>  <end base>  <stem size>

You may want to try our software by pasting the sample rna data file as input. The 2-D drawings of the two RNA structures in the sample data can be found here, RNA 1 and RNA 2.


The input data must be well-formed or the program will core dump, and you'll get no output (this is a prototype version, we're still working on a more stable version of the program)

Alignment Input Form

Please fill out this form and submit it. Thank you.

Enter you name:
Enter your e-mail address:
Enter your web site (optional):
Paste your RNA data here: