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