PMcomp tRNA example

This simple example shows a structural alignments of two tRNA sequences using 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
The resulting dot plots will look approximately like this
dot plot for DF1140 dot plot for DA0980
Note that the cloverleaf structure is hardly visible in the individual dot plots.

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