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Islander Database of Genomic Islands.

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Kelly Williams

(925) 294-4730

Corey Hudson

(925) 294-1575

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The tmRNA Website
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Sandia Biology

Islander: Conventions

Sequence Collection. 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.

Treated Genomes. The lists of treated genomes gives a list of every genome that was analyzed, to generate this list of genomic islands.

Naming convention. 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 and Eco655.45.2S

Host. This is the name (according to NCBI) of the strain into which this island was integrated.

Replicon accession. This is the GenBank accesion for the replicon into which this island was integrated.

Lineage. This is the NCBI taxononmy string for the strain into which this island was integrated.

Length. 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.

Integration site. This is the tDNA (tRNA/tmRNA) into which the island integrated.


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