pmcomp
.
The cloverleaf structure of tRNA is often not predicted correctly by RNA secondary structure prediction programs (especially when co-axial stacking is neglected). Here we use the DF1140 and DA0980 sequences from Mathias Sprintzl's tRNA database.
> DF1140 GAA MYCOPLASMA CAPRIC. EUBACT GGUCGUGUAGCUCAGUCGGUAGAGCAGCAGACUGAAGCUCUGCGUGUCGGCGGUUCAAUUCCGUCCACGACCACCA (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).... > DA0980 TGC THERMOPROT. TENAX ARCHAE GGGCCGGUAGUCUAGCGGAAGGACGCCCGCCUUGCGCGCGGGAGAUCCCGGGUUCGAAUCCCGGCCGGUCCA (((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).The dot bracket strings shows the correct clover-leaf fold of both sequences. By clicking the following links you can submit the two sequences to our fold server fold DF1440 fold DA0980
Folding both sequences using
RNAfold -p -noLP
and comparing the two resulting pair probability matrices using
pmcomp.pl DA0980_dp.ps DF1140_dp.ps
yields the following alignment and structures
GGGCCGGUAGUCUAG-CGGAAGGACGCCCGCCUUGCGCGCGGGAGAUCCCGGGUUCGAAUCCCGGCCGGUCC---A ((((((((.((((..-.....)))).(((((.......)))))..)..(((((.......))))))))))))---. GGUCGUGUAGCUCAGUCGGUAGAGCAGCAGACUGAAGCUCUGCGUGUCGGCGGUUCAAUUCCGUCCACGACCACCA ((((((((.((((........)))).(((((.......)))))..)..(((((.......))))))))))))....Thus
pmcomp.pl
finds the correct structure except for
one additional isolated base pair.
Ivo Hofacker <ivo@tbi.univie.ac.at>
Last modified: 2004-01-28 09:06:54 ivo