The TIGER & Islander database resource for bacterial and archaeal genomic islands

<b>gi_db.tsv:</b> We downloaded 458,681 prokaryotic genomes from GenBank that could be assigned to GTDB release 214 species. To generate an island database, we applied two orthogonal island finding algorithms notable for their precision in mapping island termini: Islander 1.0, limited to finding single-contig islands in tRNA/tmRNA genes, and TIGER 2.0, which compares to reference genomes and can detect cross-contig islands. Additional software resolved overlaps and tandem arrays and typed islands. This yielded 1,758,690 island assignments contained in this dataset.<br>Column Fields:<b>·#ID: </b>Island ID. Convention: three parts separated by periods: 1) the nine-digit portion of the assembly ID. 2) the size of the island rounded to the nearest kbp. 3) the gene context of the island (see https://doi.org/10.1093/nar/gkaa156). When multiple islands would have the same name by this convention, a distinguishing serial number is added as a fourth part.· <b>coordinates</b>: GenBank accession and genomic coordinates (start and stop) of the island (separated by '+' if on a split contig)· <b>source</b>: The software which predicted the island: Islander, Tiger. Those labeled "Inferred" come from resolution of tandem island arrays but did not have direct Tiger support.·<b> type</b>: Whether island is a phage, ICE, or unknown· <b>score</b>: Support score with higher values indicating more confidence.· <b>composition</b>: simple, cross or circleJxn: simple indicates the island was found intact on a single contig, cross indicates the islands start and stop are on separate contigs, circle junction indicates the island was sequences as an excised element.· <b>tiger_support</b>: number of reference genomes found to lack the island (att site preservation with no islands integrated within). This number will be 0 for islands found with only Islander.· <b>integrases:</b> gene ID of the integrase(s) within the island boundaries· <b>tRNA_site_dupe</b>: details on islands integration in tRNA genes if available. Only available for Islander tRNA calls. denotes if 3' or 5' fragment of tRNA gene found at end of island. '.' denotes island was not found in a tRNA· <b>attL</b>: the sequences flanking the attachment sites and the predicted attachment sites themselves. sequences are separated by '/'. attL are the sequences to the left of the island/the left att site/ and some of the leftmost portion of the island sequence.· <b>attR</b>: the sequences flanking the attachment sites and the predicted attachment sites themselves. sequences are separated by '/'. attR are the sequences to the right of the island/the right att site/ and some of the rightmost portion of the island sequence.·<b> taxonomy:</b> GTDB taxonomic assignment of the genome (see https://doi.org/10.1093/nargab/lqaf019)<br><b>Table_1.tsv</b>: Genomes analyzed. The table has four tab-separated fields: 1) NCBI assembly ID and version; 2) Genetic code (see https://wikipedia.org/wiki/List_of_genetic_codes); 3) Number of islands found (see database file); 4) supplemented GTDB r214 taxonomy (see doi:10.1093/nargab/lqaf019)