Align sequence on secondary strcuture

[NicoBxl]

Hi guys,

Anyone knows if a tool to align sequence (RNA, DNA) on a secondary structure exists ? It's only for visualization of the alignment on a known structure.

Thanks,

N.

[sphil]

For secondary structure based alignments look at http://expasy.org/tools/#secondary.
Hope that helps. Else if you want to do this for tertiary u can use modeller, for instance.

best,


Phil

[NicoBxl]

Thanks, but it's ok for the structure (I have it). What I want to do is align sequencing reads on this structure and see where the reads aligned on it.

[NicoBxl]

nobody knows ? I think such a tool will be useful

[me_myself_andI]

In the case of RNA you could probably use Infernal and an Rfam model of your choice to align it against your RNA in question.


Andreas