Diane Stothard wrote:
>> I was wondering what the consensus feeling is in this group for using
> structure as a guide for aligning rRNA gene sequences. I personally feel it is
You, of course, already know how I feel about this.
1) using secondary structure presupposes that the models being used for
alignment purposes are correct notwithstanding that the models are not proven
correct for the tax(on/a) under consideration and that said thermodynamic models
have been suggested as naively incorrect by others.
2) given the foregoing, secondary structure can be used effectively in the
conserved regions of the gene only - yet in these regions of the gene we really
don't need its help.
3) as phylogeneticists we are interested in uncovering patterns not imposing
patterns - use of secondary structure imposes patterns, I would argue
> necessary in order to insure comparison of homologous sites, but I have met
> many people that do not believe in secondary structures and therefore, align
> their sequences randomly (i.e., by base letter). I would especially appreciate
This is highly unfair and a gross mischaracterisation. The use of software like
Malign which is explicitly based on a parsimony optimality criterion using the
Needleman-Wunsch dynamic algorithm is hardly RANDOM! Nor does levelling such
a slander make it so.