How to upload sequences
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.
Click ''Upload sequence`` at the top of a page and choose the host organism from the drop-down menu. The sequence may be pasted in raw or fasta format. The sequence should be a valid mRNA sequence, i.e. it should be divisible by 3, deprived of nonsense codons (except the one at the end), and longer than 12 codons. To run the simulation of ribosome movement and calculate translational parameters, the time of translation initiation should be provided. Translation times of individual codons are those of the host organism. Optionally, you may also provide an estimated mean mRNA lifetime and compute the number of produced proteins from a single transcript during its lifespan.
By clicking "Generate ribosome speed splots" you may display plots of ribosome speed (in aa/sec) in relation to the uploaded coding sequence. If the sequence is not too short, 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...".
