I need some information on the mysterious "taking secondary structure
into account" when creating multiple alignments of 18S rRNA genes.
My educated guess on the process is to mark known stem sequences on
one sequence in the alignment, ie human, and then look for
palindromic sequences in similar regions of the other sequences in
the alignment and adjust the alignment to match them with the known
stem. Is this how it is done?
does anyone have any good references for this?
Can anyone direct me to references containing good information on
known 18S secondary structures (I am interested in yeast and
animals)?
Thanks in advance for the help. Jim Garey garey at next.duq.edu
