Prediction of signal recognition particle RNA genes

We describe a method for prediction of genes that encode SRP RNA. A heuristic search for the strongly conserved helix 8 motif is combined with covariance models that are based on previously known SRP RNA sequences. By screening available genomic sequences, we have identified a large number of novel SRP RNA genes and we can account for at least one gene in every genome that has been completely sequenced. Novel bacterial RNAs include that of Thermotoga maritima that, unlike all other non-gram positive eubacteria, is predicted to have an Alu domain. We have also found the RNAs of Lactococcus lactis and Staphylococcus to have an unusual UGAC tetraloop in helix 8 instead of the normal GNRA sequence. An investigation of yeast RNAs reveals conserved sequence elements of the Alu domain that aid in the analysis of these RNAs. Inspection of the human genome reveals only two likely genes, both on chromosome 14. Our method for prediction of SRP RNA genes is the first convenient tool for this task that demonstrated to be efficient and accurate and it should be therefore helpful in genome annotation.