Format

Send to

Choose Destination
Nucleic Acids Res. 2015 Jan;43(Database issue):D48-53. doi: 10.1093/nar/gku1072. Epub 2014 Nov 5.

Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes.

Author information

1
Sandia National Laboratories, Department of Systems Biology, Livermore, CA 94550, USA.
2
Sandia National Laboratories, Department of Systems Biology, Livermore, CA 94550, USA kpwilli@sandia.gov.

Abstract

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

PMID:
25378302
PMCID:
PMC4383910
DOI:
10.1093/nar/gku1072
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center