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. 2011 May 30;39(16):6886–6895. doi: 10.1093/nar/gkr335

Figure 1.

Figure 1.

(A) Recoding scheme. The table shown represents the di-nucleotide to amino acid symbol recoding scheme. Rows correspond to the first letter of the di-nucleotide, while columns to the second. For example the di-nucleotide ‘AC’ is recoded to ‘E’. (B) BlosumR log-odd matrix. The matrix assigns a score for each possible substitution between di-nucleotides pairs. (C) BlosumN log-odd matrix. The matrix assigns a score for each possible substitution between nucleotides pairs. (D) BlastR pipeline. Rfam seed alignments are used to estimate a log-odd matrix (BlosumR). BlastP is then used along with BlosumR to search recoded RNA query sequences against a similarly recoded RNA database.