Alignment programs

Mark Siddall mes at zoo.toronto.edu
Thu Dec 21 00:33:57 EST 1995

In article <carmean-1512951828090001 at berbee.botany.ubc.ca> carmean at sfu.ca (Dave Carmean) writes:
>I find it interesting that there is no discussion here of using homology
>(such as secondary structure) to align sequences.  Karl Kjer has been
>working on this aspect of alignment.

I think that secondary structure is interesting.
I am concerned though about the assumptions it makes.
That is, much of the SSU rDNA work which purports to use
secondary structure in assessing alignments fails to acknowledge
that these are model-based and that there are vanishingly few
models to work with.
I mean is it reasonable to be using a murine model for ciliates?
Moreover, there is the problem (like the Ribosomal Database
Project) wherein you end up with an upsidedown pyramid of knowledge.
So much becomes predicated on what preceded it.  How would those homology
statements look if the models and database began with anthozoans, or 
with trypanosomes for example?

Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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