How to run simulation
Make sure that you have Java version 1.7 or higher plugged into your browser. Note, that on some computers it might be necessary to turn off your antivirus program, as they may be hypersensitive to some regular applet actions.
The top part of the applet displays transcript coding sequence, which may be navigated by appropriate buttons from the control panel. Clicked codon is underlined and its details (mean translation time in ms, encoded amino acid and alternative synonymous codons with their translation times in ms) appear below. Choose any of the synonymous codons to mutate the sequence. You may also replace the chosen codon by a non-synonymous one by typing it in the window ``Non-synonymous codon'' and clicking ``Mutate''. Note, that all codons should be sense, with exception of humans for which UGA within sequence codes for selenocysteine. All mutated positions of the coding sequence are shown in red frames. After clicking on such a position the original codon is shown in the bottom right corner of the applet; clicking the ``Mutate'' button again undo the mutation.
To copy the displayed sequence at any time, use "Copy sequence to clipboard" button - the sequence will be stored in your cache memory. You may use Ctrl+V or "Paste" to retrieve it from the clipboard and place in a text file or upload at the Transimulation "Upload sequence" page.
To run the simulation of ribosomes' movement use ``Play'', ``Pause'', and ``Stop'' buttons. Buttons ``Backwards`` and ''Forwards`` move the simulation by 1 step in a given direction. Slider ''Faster/Slower`` regulates the speed of simulation and the size of a step. The actual time of simulation (in ms) is displayed in the center of the application. Ribosomes are pictured as blue rectangles covering 5 codons upstream and 5 downstream from the active side, which is marked by a blue dot. The simulation starts by placing the ribosome active site upon the initial codon and then moving it from one codon to another only if it has spent a required amount of time for translation of the current codon and the subsequent codon is vacant. The successive ribosome attaches to the initial codon after the elapse of time interval equal to the translation initiation time. If the original sequences are used, ribosome collisions will not occur during simulation, as only collision-free genes were retained in the database. Otherwise, the ribosome blockage may take place. In such a case the simulation stops and active sites of collided ribosomes are indicated by red exclamation marks.
By clicking "View ribosome speed plots" you may view precomputed plots of ribosome speed (in aa/sec) in relation to the original coding sequence. The plots are generated for seven different sizes of the smoothing sliding-window: 1 (for no smoothing), 2, 5, 10, 20, 30 and 50. Mean translation speed is also displayed and enables easy identification of ribosome acceleration/deceleration regions. For high resolution images right-click on the plot and choose "Save image as...".
