Stop that transcription! In bacteria, transcription termination can occur by the Rho-independent and Rho-dependent mechanisms. When annotating new phage genomes, the CPT has traditionally focused on identifying likely Rho-independent signals using the TransTermHP tool. Now, we have expanded the ability to look for rho-dependent transcription termination signals in CPT Galaxy with the tool published by Di Salvo et al.
The RhoTermPredict tool predicts these sites using a consensus motif defined from three organisms: E. coli, B. subtilis, and S. enterica. Simply feed the tool a nucleotide FASTA file to receive three outputs: the coordinates for the predicted sites as a .csv file, a text file with detailed prediction information, and a GFF3 file that can be piped to Apollo for contextual viewing.
Added by Anthony Criscione, the RhoTermPredict tool can be found in the Functional Prediction section under Domains and Signals. Please email the support team if you have any questions!