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The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource.

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The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources.

INTRODUCTION

GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms. It has now become the home for all pathogen genomes sequenced at the WTSI, as well as several related pathogen genomes from other institutes, and also provides a repository of genome sequences of pathogenic organisms to the wider scientific community.

GeneDB provides comprehensive coverage and a systematic approach to pathogen genome annotation, by incorporating and standardizing, data from numerous sources. Currently GeneDB hosts the sequences and associated annotation of 41 organisms, including bacterial, protozoan, helminth and arthropod genomes, making it the largest multi-organism database of curated parasite genomes.

The common factor between the genomes is the huge health and economic impact that these organisms have on humans and animals around the world. Malaria is a major cause of human mortality, and is represented on GeneDB by the Plasmodium falciparum genome, as well as genomes of several non-human Plasmodium species.

Chagas disease American trypanosomiasisleishmaniasis, schistosomiasis and human African trypanosomiasis also known as sleeping sickness are four of the Neglected Tropical Diseases identified by the World Health Organization http: Of the bacterial genomes on GeneDB, 13 are pathogenic to humans. Within the database, there are 34 finished and non-contiguous finished genomes and 7 ongoing sequencing projects Table 1. Automatic pipelines generate the majority of these genomes, including annotation transfer from closely related, manually annotated species.

Yellow indicates improved high-quality draft; cyan indicates non-contiguous finished; green indicates finished. Project type is based on categories defined in 1. Recently, the resource has undergone a complete re-implementation, with many new features added. First, to make curation, and particularly cross-organism curation, easier, the data are stored in a large multi-organism Chado database 2.

The use of Chado enables data to be structured in a way that allows rapid, flexible Athens georgia dating free article submission tools today consistent annotation of any features of a sequence. Second, the website has been modernised to provide a more intuitive and consistent navigation, browsing and searching across all organisms. Currently, the website has an average of unique users per day.

Programmatic access to the data has also been extended by means of web services, which are used to drive some of the more dynamic page elements and to provide data upgrades to other linked resources.

GeneDB is a database of annotated genomes or genomes undergoing active annotation. We focus on the rapid release and simple, rapid access, to reference genomes, with a depth of annotation and curation that is not found on other databases [such as ENA-EMBL 3 and GenBank 4 ]. Other -omics data is hosted elsewhere, allowing GeneDB to focus on the annotation of reference genomes from the published literature and user comments see Curation section.

This also enables users to explore a genome in detail, particularly in conjunction with the genome-browsing tool, Artemis see below 5with detailed and up to date curation available for every individual gene in a simple to navigate and consistent layout.

The simple layout and page design means that data are presented to users extremely rapidly. As part of a collaborative effort with the EuPathDB group of databases http: The same procedure is used for Plasmodium species parasites, which are sent to PlasmoDB 7 ; http: In addition, user comments submitted on genes in TriTrypDB and PlasmoDB are automatically forwarded to GeneDB for review and potential integration into the annotation, providing an effective mechanism for reactive curation.

A new collaboration with SchistoDB http: It is also the platform on which changes, directed from those sites, are implemented. Currently GeneDB is the only database to host multiple flatworm "Athens georgia dating free article submission tools today."

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GeneDB now holds the genome sequences of 9 apicomplexans, 3 of them human pathogens; 12 kinetoplastid protozoans, 7 of them human pathogens; 3 parasitic Athens georgia dating free article submission tools today, all human pathogens; and 16 bacterial species, 13 of them either human pathogens or opportunistic human pathogens. Table 1 shows the current status of the genomes in GeneDB. This allows concurrent annotation of multiple organisms in a central data store, and enables curators to make cross-organism annotations.

Several types of annotation are currently performed on genomes once they have been loaded into the database. These can be loosely broken down into automated and manual annotations. Automated annotations resulting from bioinformatics studies are fed into the database via the means of specialised loader programs, wrapped in PERL or BASH scripts.

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