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Here is what I know so far:

  1. Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones.
  2. There are stem regions in the S16 which I suspect are much less variable than the loops.

And here are my questions:

About 1., it is this the usual procedure?

About 2., do people use the loops or the stems to construct a phylogenetic tree? It they use stems, do they consider the coupling between stem bases? And, if they do so, where can I get a "map" of this coupling (preferably in a parseable form, not an image)?

In the other hand, is it correct to use a simpler nucleotide substitution model? which one?

Thanks in advance for any hints.

  1. Lukjancenko O, Wassenaar TM, Ussery DW. 2010. Comparison of 61 Sequenced Escherichia coli Genomes. Microbial Ecology, 60:708-720, doi:10.1007/s00248-010-9717-3.
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up vote 6 down vote accepted

OK, first of all do not use CLustalX to align the sequences. It is a very old algorithm and is outperformed by just about any modern aligner (including its descendent, clustal omega, and t-coffee, mafft, kalign etc etc).

As for 1) that depends on what you want to do, there is no perfect solution. What question are you trying to answer? If you want a tree with species-level resolution, use all sequences. If you don't need that high a resolution, choose a representative sequence from each order or genus or whatever. In all cases, remember to use a significantly different sequence as an outlier.

As a general rule, I would use the entire sequence to build a tree, both the stems and the loops. To include structural information in your alignment you may want to check out r-coffee from the t-coffee suite.

Finally, you don't really want to use a nucleotide substitution model. Most such models assume that the sequence codes for protein and are not suitable for non coding RNAs.

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Thanks for pointing to t-coffee! – dsign Sep 21 '12 at 3:05

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