A tool for prediction of conserved secondary structure of a set of homologo
us single-stranded RNAs is presented, For each RNA of the set the structure
distribution is calculated and stored in a base pair probability matrix, G
aps, resulting from a multiple sequence alignment of the RNA set, are intro
duced into the individual probability matrices. These 'aligned' probability
matrices are summed up to give a consensus probability matrix emphasizing
the conserved structural elements of the RNA set. Because the multiple sequ
ence alignment is independent of any structural constraints, such an alignm
ent may result in introduction of gaps into the homologous probability matr
ices that disrupt a common consensus structure, By use of its graphical use
r interface the presented tool allows the removal of such misalignments, wh
ich are easily recognized, from the individual probability matrices by opti
mizing the sequence alignment with respect to a structural alignment. From
the consensus probability matrix a consensus structure is extracted, which
is viewable in three different graphical representations. The functionality
of the tool is demonstrated using a small set of U7 RNAs, which are involv
ed in 3'-end processing of histone mRNA precursors. Supplementary Material
lists further results obtained. Advantages and drawbacks of the tool are di
scussed in comparison to several other algorithms.