Gardenia

Multiple sequence alignment for RNA secondary structures

Gardenia is a software tool for comparing and aligning RNA structures. The algorithm takes into account both the primary structure and the secondary structure to build an accurate multiple alignment. The edit scheme is described here.

Example

     >sequence 1
     GGGGCUAUAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGCAGGAGGUCUGCGGUUCGAUCCCGCAUAGCUCCACCA 
     (((((((..((((........)))).(((((.......))))).....(((((........))))))))))))...

     >sequence 2
     UCCUCGGUAGUAUAGUGGUGAGUAUCCGCGUCUGUCACAUGCGAGACCCGGGUUCAAUUCCCGGCCGGGGAG
     (((((((.......((((.......))))((((((.....)).))))(((((.......)))))))))))).

     Alignment

     sequence 1        (((((((     ..((((........)))).(((((.......)) ))).....(((((.
     sequence 1        GGGGCUA-----UAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGC-AGGAGGUCUGCGGU
     sequence 2        UCCUCGGUAGUAUAGUGGUG-AGUAUCCGCGUCUGU--CACAUGCGAGA----CCCGGGU
     sequence 2        (((((((.......((((.. .....))))((((((  .....)).)))    )(((((.
                           *       ***    *  *     *** ***     ** ** **     *   ***

     sequence 1        .......))))))))))))...
     sequence 1        UCGAUCCCGCAUAGCUCCACCA
     sequence 2        UCAAU-UCCCGGCCGGGGA--G
     sequence 2        ..... .)))))))))))) 
                       ** **  * *        *   

Availability

Web interface: click here.

Download: gardenia.zip and read me. You need a C compiler to build it. Gardenia is freely distributed under the GNU General Public License.

Reference

Alignment of RNA structures. Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(2): 309-322, 2010