A tool for designing capture or control probes for use in the RAP assay. This tool will allow you to design probes for a single RNA or batch across many RNAs as well as layout the probes on a custom microarray and optimize primer sequences at the ends of each probeset for selective amplification from complex synthesis pools. For a full description of the probe design process, see the RAP protocol page.
A method for detecting translated regions using ribosome profiling data. The RRS measures ribosome release at bona fide stop codons to detect translation through ORFs. The program can score individual ORFs or identify the maximum RRS for any ORF within a transcript. This method robustly distinguishes between protein-coding genes and non-coding RNAs.Download the RRS Program.
To identify all possible ORFs within a transcript for input into the RRS program, Dowload the ORF finder utility.