Figure 2

Tests for identifying stalling amino acids. The position of peak in the RD/mRNA profile is marked by a blue arrow. The USR corresponding to the peak is the upstream sequence of 31 codons which codes for the 31 amino acid that occupy the tunnel when ribosomes stall at the peak position. (A) In the first test, the frequency of each amino acid upstream of real peak positions is compared with its frequency in the 31 codons upstream of random positions. The number of randomly drawn positions per profile is equal to the number of real peaks in the original profile (see details in the Methods). (B) The additional test is performed for bacteria. In case a sequence that resembles the SD sequence was observed 8-11 bases upstream from the peak position, the peak was excluded from the analysis.