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Figure 2 | BMC Bioinformatics

Figure 2

From: ACID: annotation of cassette and integron data

Figure 2

Logistics of String search for the identification of attC sites. (A) Search for the nearly invariant nucleotides of the inverse core (AAC) and core (GTT) sites on the bottom DNA strand (TTG and CAA) (B) Assign 1 point per match between the flanking repeats of the attC sites (R' and R"), excluding the three nearly invariant nucleotides. (C) Assign 1 point per match between the inner repeats of the attC sites (L' and L"). (D) Score 1 point for the presence of the typical extra-helical base, defined here as E and, (E) Score 1 pt for each mismatch in the 2 bp adjacent to the R' repeat referred to as site S. Final scores are divided by the total possible score and are reported as percentage values.

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