FIGURE 3.

Evaluating an alignment with subgroups. (A) The Rfam secondary structure consensus (SS_cons) is shown in bracket annotation with “<” and “>” indicating a base pair. The Pfold secondary structure prediction (Pfold) is shown in bracket annotation with “(” and “)” indicating a base pair. Each base pair of the Pfold secondary structure prediction is evaluated in relation to the Rfam SS_cons as consistent (green), inconsistent (red), or novel (yellow). (B) The SARSE editor window showing the mir-399 alignment with Rfam structure annotation (SS_cons) and two subgroups (SS_1 and SS_2). The evaluation shows that base pairs of one subgroup differ from the Rfam SS_cons (colored in red). The alignment is colored as indicated by the color code shown below the editor window, where the shading indicates the prediction reliability of a given base pair. (C) Schematics of the “alistem” plot. The rectangle is a representation of the alignment, and the triangle below is used to show base pair. (D) “Alistem” plot for the Pcluster-evaluated mir-399 alignment with alignment length shown above the plot.