Preferred and avoided codon pairs in three domains of life

BMC Genomics

Table 3 The top 10 most conserved preferred codon pairs in the organisms studied

12 ↑ codon pairs	%	log₂(obs/exp)		A – B	type
		ORFeome (A)	genome (B)
GGGCUU	76	0.99	0.44	0.55	1_P
GAGCAG	70	0.51	0.64	-0.13	1_P
GGGCAU	69	0.83	0.39	0.44	1_P
UUUGAA	66	0.31	0.12	0.19
GACAGC	64	0.70	0.21	0.49	2_P
UUUGCC	64	0.51	0.07	0.44	4_P
GGAACA	64	0.82	0.52	0.30
UACAAC	64	0.58	0.36	0.22	2_P
AUCAUC	64	0.42	0.53	-0.11	2_P
CUUUCU	61	0.91	0.29	0.61	3_P

Codon pair containing out-frame UAA or UAG triplets on the sense and/or antisense strand are marked in bold. The observed/expected ratios in logarithmic scale for each codon pair in the ORFeome and genome are shown. % – the percentage of organisms in which the codon pair is significantly preferred. A – B – difference between log₂ (obs/exp) ratios in the ORFeome and the genome. A – B > 0 represents a stronger effect on the ORFeome level. For the preferred pattern types see Table 4. For the full lists of codon pairs preferred in at least 50% of the organisms studied see [additional file 2].

ISSN: 1471-2164