Looking For Archeal 23S Rrna Structural Alignment

Question

[Peter]

Hi Biostar,

does anybody know where I can download a structure annotated 23S rRNA alignment for Archea? The silva and the RDB databases do not provide a structure line (e.g. in stockholm format) in the download files for their alignments. However RDB says to use infernal for alignment, so they must have the consensus structure information somewhere..

best wishes, Peter

Answer 1

[Cliff Beall]

Sorry, probably not useful to you, but might be to someone else. The RDB has stockholm files (fairly well hidden) on their resources page: http://rdp.cme.msu.edu/misc/resources.jsp, together with instructions for using infernal.

Unfortunately for you they only have the small subunits.

It looks to me like the SILVA database has secondary structure info that you can see in arb. Don't know how to export to stockholm, though.