PMmulti Ires example

The follwing example is taken from a previous study of conserved RNA secondary structures in Picornaviridae viruses (Witwer, Rauscher, Hofacker, Stadler, NAR 29, 2001). In the study different genera of picornaviridae were treated individually because sequence alignments accross different genera proved to be too unreliable. However, visually the Ires regions of e.g. Aphtovirus and Cardiovirus looked quite similar. In the paper a manual alignment was used to demonstrate the structural conservation between Aphtovirus and Cardiovirus.
Here we use the same data as input for pmmulti.


> PIFMDV2
GCAUGUUGGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCAUGUCCUAACGGACCCAACAUGU
> FAN133359
GCAUGACGGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCACACGGGCCCGUCAUGU
> FMDVALF
GCAUGAUGGCUGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUCACGGACCCAUCAUGC
> FDI251473
GCACGCAAGCCGCGGGAACUCCCCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUUCUCUGAACCUUGCGUGU
> MNGPOLY
CCUUUGCAGGCAGCGGAAUCCCCCACCUGGUGACAGGUGCCUCUGCGGCCGAAAGCCACGUGUGUAAGACACACCUGCAAAGG
> EMCBCG
CCUUUGCAGGCAGCGGAAAUCCCCACCUGGUAACAGGUGCCUCUGCGGCCAAAAGCCACGUGUAUAAGAUACACCUGCAAAGG
> TMEPP
CACACAAAGGCAGCGGAACCCCCCUCCUGGUAACAGGAGCCUCUGCGGCCAAAAGCCACGUGGAUAAGAUCCACCUUUGUGUG

To repeat the experiment simply fold the above sequences using
RNAfold -p -noLP
Run pmmulti.pl on the dot plot files containing hte pair probabilities
pmmulti.pl *_dp.ps
The text output should look approximately like this:


TMEPP             CACACAAAGGCAGCGGAACCCCCCUCCUGGUAACAGGAGCCUCUGCGGCCAAAAGCCACGUGGAUAAGAUCCACCUUUGUGUG
    7             (((((((((((((.((.......((((((....)))))))).))))(((.....)))..((((((...)))))))))))))))
EMCBCG            CCUUUGCAGGCAGCGGAAAUCCCCACCUGGUAACAGGUGCCUCUGCGGCCAAAAGCCACGUGUAUAAGAUACACCUGCAAAGG
    1             (((((((((((((.((.......((((((....)))))))).))))(((.....)))..((((((...)))))))))))))))
MNGPOLY           CCUUUGCAGGCAGCGGAAUCCCCCACCUGGUGACAGGUGCCUCUGCGGCCGAAAGCCACGUGUGUAAGACACACCUGCAAAGG
    5             (((((((((((((.((.......((((((....)))))))).))))(((.....)))..((((((...)))))))))))))))
FDI251473         GCACGCAAGCCGCGGGAA-CUCCCCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUUC----UCUGAACCUUGCGUGU
    3             ((((((((((((((((..-.....(((((....))))).)))))))(((.....)))..((((----...)))))))))))))
FMDVALF           GCAUGAUGGCUGUGGGAA-CUCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCC---UCACGGACCCAUCAUGC
    4             ((((((((((((((((..-.....(((((....))))).)))))))(((.....)))..((((---....)))))))))))))
FAN133359         GCAUGACGGCCGUGGGAA-CUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCC---ACACGGGCCCGUCAUGU
    2             ((((((((((((((((..-....((((((....)))))))))))))(((.....)))..((((---....)))))))))))))
PIFMDV2           GCAUGUUGGCCGUGGGAA-CACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCAUGUCC---UAACGGACCCAACAUGU
    6             ((((((((((((((((..-....((((((....)))))))))))))(((.....)))..((((---....)))))))))))))
CONSENSUS_SEQ     NNNNNNNNGNNNNNGGAANNNCCNNCNUGGUNACANGNNCCNNNGNGGCCRAAAGCCANGNNNRUANNNYNNNCCNNNNNNNN
CONSENSUS_STR     (((((((((((((.((..~.....(((((....))))).)).))))(((.....)))..((((~~~....)))))))))))))

To obtain the drawings shown in figure 3 of the paper, the resulting alignment was once more used as input to RNAalifold.
By clicking the following link you can submit the alignment to our alifold server.

Ivo Hofacker <ivo@tbi.univie.ac.at>

Last modified: 2004-01-28 09:04:11 ivo