. Entries from 3699 RefSeq prokaryotic genome, plasmid or bacteriophage projects available in Nov 2012 were searched with the Islander
Island-finding software. Some genomic islands proved unconvincing, based on their presence in phages or plasmids, their length, and other attributes. These are provided in the list of false positives
. The lists of treated genomes
gives a list of every genome that was analyzed, to generate this list of genomic islands.
. The general naming convention is first letter of the genus name, first two letters of the species name, a strain disambiguator, period, the length rounded to the nearest kb, followed by the one-letter codon designator (with X for tmRNA and B for the initiation codon). For example, Escherichia coli
str. K-12 substr. MG1655 was the 837th E. coli strain that the Islander database encountered, and it has a genomic island that is 10,215 bp and integrates into a tRNA-Arg(CCT), the name is therefore Eco837.10R
. In cases where a genome has multiple cases of nearly the same length, integrating into the same tRNA, these are subsequently numbered, for example Escherichia coli
O157:H7 str. EDL933 has two islands that integrate into tRNA-Ser, one is 45,117 bp and one is 45,185 bp. Their names are Eco655.45.1S
. This is the name (according to NCBI) of the strain into which this island was integrated.
. This is the GenBank accesion for the replicon into which this island was integrated.
. This is the NCBI taxononmy string for the strain into which this island was integrated.
. This is length of the genomic island. This length goes from the anticodon or (7-bp) junction breakpoint sites in the tDNA to the tDNA resolving position in the displaced fragment.
. This is the tDNA (tRNA/tmRNA) into which the island integrated.