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Table 1 Illustrative examples of emission scores in the three models.

From: Noncoding RNA gene detection using comparative sequence analysis

  1. Scores (in bits) are given both as log-odds scores respect to an IID model of no alignment, and as log-probabilities (in parentheses). For the COD model pairing of synonymous codons (e.g. AAC/AAU both coding for Asn, or UCU/AGC both coding for Ser) have positive scores, even though they include up to three mismatches, whereas just one mismatch produces a negative score when the two codons are non-synonymous (e.g. AAC/AUC coding for Asn and Ile respectively). For the RNA model base-paired positions score better than they would do with the OTH model, while two positions that do not form Watson-Crick pairs have a worse score than two mismatched positions that do form Watson-Crick pairs.