Figure 1From: Noncoding RNA gene detection using comparative sequence analysisThree pairwise alignments of identical composition with identical number of base substitutions can be classified by distinctive patterns of mutation caused by different selective constrains: the position-independent null hypothesis (top), a coding region (middle), or a structural RNA (bottom). We indicate how each alignment is scored according to the model that best fits the pattern of mutations: one position at the time for OTH, one codon at the time for COD (integrated over all six possible frames), and as a combination of base-paired positions and single positions for RNA (integrated over all possible secondary structures).Back to article page