Several years ago, I was working on a project where I had to align a number of ribosomal RNA sequences by secondary structure. It was very time-consuming and patience-taxing, mostly because I had to do a lot of things by hand and eye. I wasn't aware of any reasonably good automated way to do it, though I did use RNAStructure to help with some variable regions. I am considering getting back into that project. Last time I was only working with 18S sequences; this time I would like to add 28S sequences, which are longer and surely more frustrating to deal with.
So I'm writing to ask: for people who have some experience at this, what method (or set of methods) work(s) best, to avoid spending weeks and months adjusting your alignment, especially where hypervariable regions and pseudoknots are concerned?
Check out the Q-INS-i mode of MAFFT, "secondary structure of RNA is considered ". (http://mafft.cbrc.jp/alignment/software/)
Hi Yedid,
You can use 4SALE to align your sequences, together with your structure.
(http://4sale.bioapps.biozentrum.uni-wuerzburg.de/). It's user friendly and you can get your alignment shortly.
You can also refer to our latest paper for more info.
http://onlinelibrary.wiley.com/doi/10.1111/j.1529-8817.2012.01213.x/abstract
HongChang
4Sale (http://4sale.bioapps.biozentrum.uni-wuerzburg.de/) can be used for such work. The alignmets which can be generated by using this software based on CLUSTALL algorithm.You may use it, if it is suitable for you.
Like Julien, I use RNAsalsa. I've never heard of 4SALE but will give it a look, as I am now trying to run secondary-structure based alignments on a large rRNA datasets (1600+ sequences) and having some problems with the downloadable RNAsalsa executables. There's also locARNA (http://www.bioinf.uni-freiburg.de/Software/LocARNA/), which I find to be quite useful for things like tRNAs.
OK, thanks to everybody who answered!
Now, which online databases have both sequences and structure files that can be read by the suggested software? In particular, I'm looking for small and large rRNA sequences from (eu)crustaceans or hexapods.
cheers,
Gabe
Short answer for everything you need is RNA Fold, a free software (or web-based interface) at http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi also check their RNA Ali fold (for alignment refinement taking cues from conserved motives). All the best!
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