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Figure 2 | BMC Genomics

Figure 2

From: Systematic identification of stem-loop containing sequence families in bacterial genomes

Figure 2

Alignment of ERIC, Pae-1, Sta-1 and Efa-1 family members. (A) A representative set elements from each family was aligned by using the HMM model as a guide. In each panel, one row corresponds to one family member (indicated on the right with its genomic position). Within each row, sequence conservation is indicated by increasing gray levels and gaps by dotted spaces; overlapping SLSs are reported as red and blue lines, the red ones indicating SLSs used to define the original HMM model for the family, the blue all the others. Darker colors indicate the SLS folding aptitude, i.e. positivity to RANDFOLD for P <= 0.005. Common secondary structures, predicted by RNAz, are reported at the bottom, just above the ruler in nucleotides: green triangles indicate stems produced by pairing complementary regions on the same strand as the identified SLSs, while brown triangles indicate the same from the opposite strand. The boxed regions highlight areas where aligned SLSs and predicted structures are in agreement. (B) Graphic representation of the RNAz predicted secondary structures.

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