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Finally, a practically fast multiple alignment tool for RNAs has arrived !
Long-awaited practical multiple alignment tool for structural RNA sequences is released by a research group of National Institute of Advanced Industrial Science and Technology (AIST) and Graduate School of Frontier Sciences, University of Tokyo. The tool is named Murlet and its web server is readily available. The source code is released under public domain.
Murlet is a practical multiple alignmet tool for RNA sequences. Whereas Murlet is yet another implementation of the Sankoff's algorithm, what Murlet differentiate from other Sankoff-based tools is that Murlet is practical in terms of computational time and memory complexity. It is fast and memory efficient sufficiently for a daily alignment routine.
Please see the figure exerpt from Murlet paper (click to enlarge).
Murlet paper is now on the advanced access of Bioinformatics.