What is Magnolia ?

Magnolia is a program suite to classify RNA sequences as protein-coding or noncoding genes by comparative analysis. It also produces advanced multiple sequence alignment for the data.

Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern. It combines two evolutionary models.

If the sequences are classified as protein coding sequences, then the nucleic multiple alignment is built from the hypothetical amino-acid sequences using ClustalW. This process is able to handle frameshifts. If the sequences are classified as noncoding RNA genes, then the multiple alignment takes into account both the primary structure and the predicted common secondary structure of the RNA sequences. This is done with the gardenia tool.

See examples.


You can use Magnolia via the web interface.


Arnaud Fontaine, Antoine de Monte, Helene Touzet.
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences.
Nucleic Acids Research 36 (Web-Server-Issue): 14-18, 2008 [pubmed]