Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

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.
share|improve this question

1 Answer 1

up vote 4 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.

share|improve this answer
    
Thanks for pointing to t-coffee! –  dsign Sep 21 '12 at 3:05

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.