Paper Info
Title
Neisseria Base: a comparative genomics database for Neisseria meningitidis.
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. Database URL: http://nbase.biology.gatech.edu
Year
DOI
Venue
2011
10.1093/database/bar035
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
Keywords
Field
DocType
genomics,genetic markers,database management systems
Genome,Neisseria meningitidis,Semantic search,Genome browser,Computer science,Neisseria,Genomics,Database schema,Comparative genomics,Bioinformatics,Database
Journal
Volume
ISSN
Citations 
2011
1758-0463
0
PageRank 
References 
Authors
0.34
13
13
Name
Order
Citations
PageRank
Lee S. Katz181.95
Jay C. Humphrey2906.55
Andrew B. Conley392.45
Viswateja Nelakuditi4181.89
Andrey Kislyuk5523.33
Sonia Agrawal681.41
Pushkala Jayaraman7132.13
Brian H. Harcourt871.48
Melissa A. Olsen-Rasmussen900.34
Michael Frace1000.34
Nitya V. Sharma1100.34
Leonard W. Mayer1271.48
I. King Jordan1372.31