Computational protocol: Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence

Similar protocols

Protocol publication

[…] Using the Free Energy Minimization method–, we conducted the modeling based on the assumption that the total free energy of a given secondary molecular structure is the sum of independent contributions of adjacent or stacked base pairs in stems. For modeling the stem-loop structures, we employed the Vienna RNA Package (, which consists of a C code library and several programs including RNAfold. The program reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout. We used the script to produce mountain plots and the Maximum Expected Accuracy method with the program CONTRAfold to predict the pseudo-knot-free structures. CONTRAfold uses the maximum P (i, j) expected accuracy approach for the predictions. We also used RNAstructure (Mathews Lab, University of Rochester Medical Center, Department of Biochemistry and Biophysics), which contains the MaxExpect program (, for the analysis. To run the programs for the prediction task, we employed an HPC Cluster based on Ubuntu 14.04.2 LTS (Trusty), Kernel 3.16.0-30-generic, using the Sun Grid Engine 6.2u5-7.3 amd64 as queue manager and scheduler to accept jobs. The programs were run on the cluster in the “trivial parallel computing” way and the results were obtained from RNAfold v. 2.19 and MaxExpect v. 5.6 linked to Perl v.5.18.2. […]

Pipeline specifications

Software tools ViennaRNA, RNAfold, CONTRAfold, RNAstructure, MaxExpect
Application RNA structure analysis
Chemicals Nucleotides