Hello Yanan - thanks for your nice email!
Yanan Jiang wrote:
I am doing RNA multiple sequence alignment and find Jalview is a very
handy tool.
That's good to hear!
But when I called these programs, they happened to align the RNA
sequences, except for muscle. Does it mean that Jalview can do RNA
sequence alignment?
Muscle is designed purely for amino acid alignment, and so will only
align RNA if it does not include uracil, and, as you surmised, will in
any case only apply an amino acid substitution matrix.
The situation is a little better with MAFFT and ClustalW - both will
align RNA happily, and MAFFT in particular will also use the identity
matrix to calculate substitution cost rather than an amino acid score
matrix.
I'm also curious about whether jalview is friendly
to RNA or not.
Jalview isn't 'unfriendly' to RNA, but it doesn't have all the tools
that someone working on RNA might like. In particular, there is no real
support for RNA secondary structure annotation. Hopefully this will be
somewhat remedied in the future, since RNA analysis is one of the focus
areas in the next phase of Jalview development (which will start in a
few months time).
Are there some research groups using Jalview for RNA study?
There are two or three groups that I know of and are in contact with,
and I also noticed that one of the citations for the new Jalview paper
concerned RNA analysis.
If you are interested in helping improve Jalview for RNA work, then
please watch the Jalview website and announcements list, try out the new
features when they appear, and tell us what you think!
all the best - and I hope we'll hear from you again in the future,
Jim.
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J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
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