Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes
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.
- Authors:
-
- Sandia National Lab. (SNL-CA), Livermore, CA (United States)
- Publication Date:
- Research Org.:
- Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1213420
- Grant/Contract Number:
- AC04-94AL85000
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 43; Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Hudson, Corey M., Lau, Britney Y., and Williams, Kelly P. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes. United States: N. p., 2014.
Web. doi:10.1093/nar/gku1072.
Hudson, Corey M., Lau, Britney Y., & Williams, Kelly P. Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes. United States. https://doi.org/10.1093/nar/gku1072
Hudson, Corey M., Lau, Britney Y., and Williams, Kelly P. Wed .
"Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes". United States. https://doi.org/10.1093/nar/gku1072. https://www.osti.gov/servlets/purl/1213420.
@article{osti_1213420,
title = {Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes},
author = {Hudson, Corey M. and Lau, Britney Y. and Williams, Kelly P.},
abstractNote = {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.},
doi = {10.1093/nar/gku1072},
journal = {Nucleic Acids Research},
number = D1,
volume = 43,
place = {United States},
year = {Wed Nov 05 00:00:00 EST 2014},
month = {Wed Nov 05 00:00:00 EST 2014}
}
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Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements
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