There are ca. 30 independent RNA families for "internal ribosome entry site" (IRES) in Rfam (http://rfam.xfam.org). I suspect larger commonalities between those families and wonder if anyone is aware of attempts to (structurally) align those sequences. Could you point me to those data?
Here's a good review that spotlights the well-characterized IRESes from RNA viruses that are grouped according to their different requirements for trans-factors, especially translation initation machinery. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706518/
I was impressed with Christian Zwieb's analysis of RNA structure after seeing him give a talk about ERNA 3D, a 3D molecular modeling software. Here's one of his publications looking at IRESes: http://www.ncbi.nlm.nih.gov/pubmed/21681504
Hope this is of some help, Stefan.
Check out "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites" and "http://www.iresite.org". They may help you with IRES.
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