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About SupeRNAlign

SupeRNAlign is a tool for flexible superposition of RNA 3D structures. Our program implements an iterative algorithm that splits RNA structures into fragments and superimposes them using existing tools (currently R3D Align, SARA, ARTS or LaJolla). Finally, the superimposed structures are saved to a .pdb file and a sequence alignment is generated.

Standalone version

For computationally intensive tasks you may consider downloading the standalone version of SupeRNAlign.

The latest version can be obtained from BitBucket repository:

Download SupeRNAlign (.zip file)

Please keep in mind that you need to install an older version of R3D Align (available here) in order to use it with SupeRNAlign.

A detailed tutorial is available.


Paweł Piątkowski <>
Jagoda Jabłońska
Janusz Bujnicki <>

International Institute of Molecular and Cell Biology

Laboratory of Bioinformatics and Protein Engineering

Trojdena 4, 02-109 Warsaw, POLAND
tel: +48-22 597 0750
fax: +48 22 597 0715