rRNA identification tools or information PLEASE!

[mm.perrineau]

Hi everybody,

I identified in my genome (by blast) 1 contig which is the rRNA genome.

Now, I am searching for tools able to tell me where is exactly all the different part: i mean the 18S/ITS1/5.8S/ITS2/28S...

I tried with RNAmmer Prediction Server.
It give me the 18S and the 28S but not the 5.8S so i guess it is a fake identification...

Or do you have any information about the structure of the rRNA sequence?
So i can find by myself the beginning and the end of each part...

I couldn't found any information !!!!

Thank you very much

[proteomania]

RNAmmer Prediction works fine, and 5.8S was intentionally excluded from the prediction, in the paper the authors wrote,

"In eukaryotes, 5S, 5.8S and 28S rRNA exist in the large subunit, and 18S rRNA in the small subunit. The 5.8S is not considered in this work."