Such sites often corresponded
to “”genomic islands”" with G-C ratios (from 34.9% to 43.1% ± 4.1) that deviate from the intrinsic H. pylori ratio of about 39%. Expected recognition sites were calculated performing simulations on model sequences with the same length for the MLS and the WGS. These model sequences were constructed based on the average proportion of nucleotides of the actual BIBW2992 research buy sequences analyzed (Additional file 1: Table S1). To establish the expected frequencies of appearance of a specific recognition site by chance, we randomized the order of the nucleotides in the model sequences and enumerated the occurrence of that specific recognition
site (see Methods for details). pylori ACY-1215 order whole genome sequences and MLS for hspAmerind
and hpEurope strains RMS Mean ± SD frequency/1.00 bp O/E ratiob Endonuclease/ Methylase Cognate recognition sitea MLS (N = 73) WGS (N = 6) Observed Expected Observed Expected MLS (N = 73) WGS (N = 6) Hpy 166III CCTC 2.7 ± 0.41 5.49 ± 0.07 2.93 ± 0.02 4.50 ± 0.03 0.50 c 0.65 Hpy178VI GGATG 1.48 ± 0.23 1.59 ± 0.03 0.81 ± 0.00 1.37 ± 0.01 0.93 0.59 Hpy17VII GGCC 1.24 ± 0.31 1.96 ± 0.05 0.98 ± 0.02 1.43 ± 0.02 0.63 0.68 Hpy188I TCBGA 1.02 ± 0.21 3.70 ± 0.03 0.81 ± 0.02 3.53 ± 0.01 0.28 0.23 Hpy188III TCBBGA 1.11 ± 0.22 3.70 ± 0.04 1.19 ± 0.02 3.53 ± 0.01 0.30 0.34 Hpy8I GTNNAC Mannose-binding protein-associated serine protease 0.40 ± 0.35 3.70 ± 0.03 0.22 ± 0.01 3.53 ± 0.01 0.11 0.06 Hpy8II GTSAC 0.00 ± 0.00 1.56 ± 0.02 0.05 ± 0.00 1.37 ± 0.01 0.00 0.04 Hpy8III GWGCWC 0.07 ± 0.12 0.66 ± 0.01 0.19 ± 0.01 0.19 ± 0.00 0.10 0.36 Hpy99I CGWCG 0.28 ± 0.06 1.13 ± 0.02 0.15 ± 0.01 0.88 ± 0.01 0.25 0.17 Hpy99III GCGC 4.62 ± 0.64 1.96 ± 0.05 3.73 ± 0.11 1.43 ± 0.02 2.36 2.60 Hpy99IV CCNNGG 1.62 ± 0.26 1.96 ± 0.05 0.70 ± 0.01 1.43 ± 0.03 0.83 0.49 Hpy99VIP GATC 5.48 ± 0.44 3.70 ± 0.03 3.19 ± 0.04 3.53 ± 0.01 1.48 0.90 Hpy99XIIP GTAC 0.37 ± 0.20 3.70 ± 0.04 0.07 ± 0.00 3.53 ± 0.01 0.10 0.02 HpyAV CCTTC(6/5) 0.58 ± 0.12 1.58 ± 0.02 0.80 ± 0.02 1.37 ± 0.01 0.37 0.58 HpyC1I CCATC(4/5) 1.94 ± 0.26 1.94 ± 0.26 1.60 ± 0.02 1.39 ± 0.01 1.22 1.01 HpyCH4II CTNAG 0.60 ± 0.28 3.70 ± 0.03 1.84 ± 0.04 3.53 ± 0.01 0.16 0.52 HpyCH4III ACNGT 0.89 ± 0.22 3.70 ± 0.04 0.34 ± 0.00 3.53 ± 0.01 0.24 0.10 HpyCH4IV ACGT 0.39 ± 0.