Islander is a comprehensive online database containing genomic islands discovered in completely sequenced bacterial genomes by the algorithm. Islands are transmitted between prokaryotic strains and therefore play a major role in genome evolution.
An island often encodes an integrase gene that specifies the island's position in the host genome. Usually integrases specify tRNA genes, and the island splits the the tRNA gene when it integrates. However the island also carries sequence that replaces the split-off portion, restoring an intact tRNA gene. Thus an island is often marked by a tRNA gene at one end, and a fragment of that gene at the other end. The islands in this database were identified using this principle through the following procedure:
:1. Search for tRNA and tmRNA genes using tRNAscan-SE and BRUCE on whole prokaryotic genomes.
:2. Search for significant hits to each tRNA and tmRNA gene using BLAST against the source genome.
:3. Narrow down hits to those containing integrase genes (required for site-specific integration into the host genome).
:4. Remove false positives (e.g., tRNA gene fragment not from end of gene, or in wrong orientation).
:5. Enter into mysql database, display on website using Perl CGI pages.
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Created 4 years ago by Anonymous