18S rRNA Alignments

[Jim Garey]

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