Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

Table 2.

Analysis of the Avoidance of Palindromes and RS of Length 4 and 6 in the Genomes of Phages

Phage Host Length (bp) Type %G + C Length 4 Length 6
Palindromes RMS Palindromes RMS
bias O/E bias bias O/E bias
PBSX Basu 27614 dsDNA 44.9 — 0.63 0 0 0.91 0
SPβc3 Basu 134416 dsDNA 34.6 — 0.63 0 0 0.89 0
PZA Basu 19366 dsDNA 39.7 - 0.67 0 — 0.57 0
α3 Esco 6087 ssDNA 45.2 — 0.59 1* 0 0.94 0
f1 Esco 6407 ssDNA 40.9 — 0.59 1* — 0.56 0
fd Esco 6408 ssDNA 40.9 - 0.65 1* — 0.56 -
fr Esco 3575 ssRNA 51.4 0 1.01 7* 0 1.00 0
G4 Esco 5577 ssRNA 45.7 - 0.68 1* 0 0.92 0
GA Esco 3466 ssRNA 47.9 0 0.84 16* 0 0.90 0
I2-2 Esco 6744 ssDNA 42.7 — 0.57 4* — 0.65 0
If1 Esco 8454 ssDNA 43.7 — 0.44 2* — 0.67 -
Ike Esco 6883 ssDNA 39.5 - 0.72 3* — 0.69 -
λ Esco 48502 dsDNA 49.9 — 0.42 1* — 0.38 —
MS2 Esco 3569 ssRNA 52.1 0 0.83 14* 0 1.04 0
MX1 Esco 4215 ssRNA 28.6 0 0.89 6* 0 1.03 0
Mu Esco 36717 dsDNA 52.1 — 0.46 1* — 0.51 —
N15 Esco 46375 dsDNA 51.2 — 0.60 1* — 0.70 -
NL95 Esco 4248 ssRNA 50.8 0 1.01 1* 0 1.06 0
P2 Esco 33593 dsDNA 51.2 - 0.70 1* — 0.66 -
P4 Esco 11624 dsDNA 49.5 - 0.70 1* — 0.77 —
φK Esco 6089 ssDNA 45.0 — 0.54 1* 0 0.85 0
φX174 Esco 5386 ssDNA 44.8 — 0.38 1* — 0.67 0
PRD1 Esco 14925 dsDNA 47.1 — 0.42 1* — 0.46 —
S13 Esco 5386 ssDNA 44.3 — 0.41 1* 0 0.64 -
T3 Esco 19680 dsDNA 50.6 — 0.51 1* — 0.44 -
T4 Esco 168900 dsDNA 35.3 — 0.55 1* — 0.78 0
T7 Esco 39937 dsDNA 48.4 — 0.33 1* — 0.53 -
HP1 Hain 32355 dsDNA 40.0 — 0.24 - — 0.63 0
PsiM2 Meth 26111 dsDNA 46.3 0 1.08 0 0 0.87 NA
D29 Mytu 49136 dsDNA 63.5 0 0.95 NA — 0.36 NA
I5 Mytu 52297 dsDNA 62.2 0 0.92 NA — 0.46 NA
PF1 Psae 7349 ssDNA 61.5 0 1.03 NA — 0.74 0
Pf3 Psae 5833 ssDNA 45.4 + 1.29 NA — 0.69 0
φCTX Psae 35559 dsDNA 62.6 0 1.08 NA - 0.84 0
PP7 Psae 3588 ssRNA 54.2 0 1.12 NA 0 1.02 0

  • Palindrome bias is the test that palindromes are more biased than the remaining words. O/E displays the ratio observed/expected of the mean rank of palindromes sorted by decreasing avoidance. RMS avoidance is the result of the Wilcoxon test that RS are more biased than the remained palindromes.

  • Abbreviations: NA, unknown RMS on the species; n*, rank of the sole RS known in the species for 4-palindromes (not enough elements for nonparametric statistics); —, underrepresentation (P-value <0.001); -, underrepresentation (P-value <0.05); 0, no bias. See Methods for species abbreviations.

This Article

  1. Published in Advance May 8, 2001, doi: 10.1101/gr.153101 Genome Res. 11: 946-958

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