SRPscan - Prediction of SRP RNA genes in genomic DNA sequences

This prediction is based on methods described in our paper Regalia et al (2002) Nucl. Acid Res. 30, 3368-3377 . Supplement to the paper is found here . The prediction method makes use of rnabob and COVE. In this web server also MFOLD is used to predict the secondary structure - this function is currently disabled, May-08.

Background on method.

1. First step: Preliminary scan

In one alternative (Fast, no mismatches) you expect your sequence to match exactly the helix 8 pattern characteristic of SRP RNA. In the other alternative (Slow ) you allow mismatches.

Fast (no mismatches)    Slow (mismatches allowed)


Select organism / RNA structure subtype:  


A. Submission of a local file in FASTA format
( If local file is specified, sequence in the textarea below will not be used! )
B. ... or by pasting sequence in FASTA or raw text format: (At present only one sequence allowed!)
Test sequences
The search may take 1-2 minutes for a single sequence.