arrow

From NeuroLex

Revision as of 11:34, 17 May 2011 by Ccdbuser (Talk | contribs)
Jump to: navigation, search



Resource:Islander

Name: Resource:Islander
Description:

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.
Other Name(s): Islander
Parent Organization: Virginia Bioinformatics Institute
Resource Type(s): database
Resource: Resource
URL: http://www.indiana.edu/~islander
Id: nif-0000-03051
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

This resource will be curated within 7 days.

For Resource Owners:
After the resource is curated, you may create a sitemap, which will help keep your registry description up-to-date and inform search engines about your resource.

Note: For a new resource, the website's URL must first be verified by a NIF curator before you may proceed.

Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site. Please login to create the sitemap. (top right)

This page uses this default form:Resource

Contributors

Aarnaud, Akash, Ccdbuser, Nifbot2



bookmark
Facts about Resource:IslanderRDF feed
CurationStatusuncurated  +
DefiningCitationhttp://www.indiana.edu/~islander  +
Definition

Islander is a comprehensive online
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.
lay on website using Perl CGI pages.
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-03051  +
Is part ofVirginia Bioinformatics Institute  +
LabelResource:Islander  +
ModifiedDate18 May 2011  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymIslander  +