Detection of horizontal transfer of individual genes by anomalous oligomer frequencies

BMC Genomics

Table 2 Putative foreign genes in genome islands

		Island hits^c
Method^a	Total putative foreign^b	Expected	Observed	Observed/Total^d
Pmm (Prochlorococcus marinus Med4)^e
Codon bias	231	28	60^*	0.260
CGS	91	11	23^*	0.253
W8	96	12	15	0.156
GC	109	13	13	0.119
Pmi ( Prochlorococcus marinus MIT9312)^e
Codon bias	272	37	56^*	0.206
CGS	118	16	29*	0.246
W8	107	15	16	0.150
GC	119	16	25^*	0.21

^a All methods used a threshold that excludes 95% of the test-native set.
^b Genes identified as foreign by the method in the given genome. Pmm has 209 coding genes in genome islands out of a total of 1713 coding genes, and Pmi has 246 coding genes in genome islands out of a total of 1810 coding genes, per Coleman et al. (2006). ^c The number of genes identified as foreign by the method that lie within a genome island. The expected number is that which would arise if the genes identified as foreign were distributed randomly throughout the genome. Asterisks indicate statistical significance to the level P < 0.001. Numbers without asterisks are not significant even to P < 0.05. ^d The fraction of total putative foreign genes identified by the method that lie within genome islands.

ISSN: 1471-2164