Alignment programs

Andrew J. Roger aroger at ac.dal.ca
Tue Dec 19 14:47:17 EST 1995

carmean at sfu.ca (Dave Carmean) wrote:
>In article <DJK4In.ELC at zoo.toronto.edu>, mes at zoo.toronto.edu (Mark
>Siddall) wrote:  [much interesting and useful material here and in related
>> However because MALIGN is so thorough it takes a lot of memory and
>> processor time.
>> So you have a choice... get your alignment quick or be rigorous in your
>> science.
>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.

There is an assumption here however- that is that secondary structures
will change more slowly than primary sequences. I think that this
is generally true but one should look out for cases where there
are secondary structures which appear identical but are shifted 
relative to primary sequence similarity. In other words, it is
possible that structures could be retained by shifting over several
bases causing you to misalign the primary sequences. One would
expect, for instance, that sometimes in stemloops that loops
could get one base smaller (by a new base-pairing at the top of
the stem) and the base of the stem could unpair. You would be left
with a stem of the same size but its alignment with homologous
stems would become problematic if stem boundaries are only paid
attention to.

It worries me when I here many rRNA advocates claim that they
have based their alignment on secondary structure and therefore
homologous alignment is assured. Homology is ALWAYS an inference-
and nothing guarantees homology- not even tertiary structures!

Andrew J. Roger

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