Unknown

Dataset Information

0

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.

SUBMITTER: Katz LS 

PROVIDER: S-EPMC3263597 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

altmetric image

Publications


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 a  ...[more]

Similar Datasets

2011-07-31 | GSE30813 | GEO
| S-EPMC5531161 | biostudies-other
| S-EPMC6599670 | biostudies-literature
2012-10-05 | GSE38033 | GEO
| S-EPMC2567348 | biostudies-literature
| S-EPMC4425860 | biostudies-literature
2009-11-11 | GSE18951 | GEO
| S-EPMC4029949 | biostudies-literature
| S-EPMC2238940 | biostudies-literature
2007-04-04 | E-TIGR-129 | biostudies-arrayexpress