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Database Commons - Neisseria Base

Neisseria Base

Citations: 5

z-index 0.00

Short name Neisseria Base
Full name A Comparative Genomics Database for Neisseria Meningitidis
Description A comparative genomics database and genome browser that houses and displays publicly available N. meningitidis genomes.
URL http://nbase.biology.gatech.edu
Year founded 2011
Last update & version 2011-09-16    
Availability Not Available
University/Institution hosted Georgia Institute of Technology
Address
City Georgia
Province/State
Country/Region United States
Contact name I. King Jordan
Contact email king.jordan@biology.gatech.edu
Data type(s)
Major organism(s)
Keyword(s)
  • comparative genomics
Publication(s)
  • Neisseria Base: a comparative genomics database for Neisseria meningitidis. [PMID: 21930505]

    Lee S Katz, Jay C Humphrey, Andrew B Conley, Viswateja Nelakuditi, Andrey O Kislyuk, Sonia Agrawal, Pushkala Jayaraman, Brian H Harcourt, Melissa A Olsen-Rasmussen, Michael Frace, Nitya V Sharma, Leonard W Mayer, I King Jordan
    Database : the journal of biological databases and curation 2011:2011
    5 Citations (Google Scholar as of 2016-01-22)

    Abstract: Neisseria meningitidis is an important pathogen, causing life-threatening diseases including meningitis, septicemia and in some cases pneumonia. Genomic studies hold great promise for N. meningitidis research, but substantial database resources are needed to deal with the wealth of information that comes with completely sequenced and annotated genomes. To address this need, we developed Neisseria Base (NBase), a comparative genomics database and genome browser that houses and displays publicly available N. meningitidis genomes. In addition to existing N. meningitidis genome sequences, we sequenced and annotated 19 new genomes using 454 pyrosequencing and the CG-Pipeline genome analysis tool. In total, NBase hosts 27 complete N. meningitidis genome sequences along with their associated annotations. The NBase platform is designed to be scalable, via the underlying database schema and modular code architecture, such that it can readily incorporate new genomes and their associated annotations. The front page of NBase provides user access to these genomes through searching, browsing and downloading. NBase search utility includes BLAST-based sequence similarity searches along with a variety of semantic search options. All genomes can be browsed using a modified version of the GBrowse platform, and a plethora of information on each gene can be viewed using a customized details page. NBase also has a whole-genome comparison tool that yields single-nucleotide polymorphism differences between two user-defined groups of genomes. Using the virulent ST-11 lineage as an example, we demonstrate how this comparative genomics utility can be used to identify novel genomic markers for molecular profiling of N. meningitidis.

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Tags

DNA
Neisseria meningitidis
comparative genomics

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Zhang Zhang [2016-04-26]
    • Lin Liu [2016-03-27]
    • Lina Ma [2015-12-31]
    • Li Yang [2015-06-26]
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