Eukaryotic genome size databases

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs

Towards a bioinformatics platform for the Musa research community : [Abstract W076]

Current experiments in genomics produce a large amount of data that needs to be organized into databases and broadly accessible. Like other species, the Musa genomics community would benefit from centralized and innovative ways to study its genome. Over the past years, genetic and genomic data (e.g. BAC, EST, Markers) have been generated and stored in databases. Several pipelines of analyses were implemented for gene, transposable element, and expression data analyses, and for comparative genomics such as ortholog predictions via a phylogenomic approach (GreenPhyl). Web tools have been developed or implemented to facilitate access to data, such as genetic makers (TropGeneDB), genetic maps (CMap), a physical Map (GBrowse), and Expressed sequence Tags (ESTtik) gene/TE predictions, and to allow online manual genome annotation (GnpAnnot). The number of tools may continue to grow, in particular with the near release of the Musa genome sequence, and the increase of Next-Generation Sequencing (NGS) facilities. The GMGC website (http://www.musagenomics.org) is a place where data can be shared, and where databases and tools can be listed in an homogeneous way to serve the Musa genomics community. It is intended to provide the researchers interested in Musa with a common set of resources in order to work more efficiently and effectively. (Texte intégral

A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

In silico Gene Characterization and biological annotation of Aspergillus niger CBS 513.88

Genome annotation is the process of estimation of biological features from genomic data. The target of a genome annotation is to identify the key features of the genome sequence particularly, the genes and gene products. The characteristics of a gene, its products, and gene prediction programs of Aspergillus niger are discussed. Although the number of genomes in genomic databases are increasing day by day, genome-wide analyses are affected by the quality of the genome annotations. This study illustrates the importance of integrative approaches for automatic annotations of genomes of Aspergillus niger by computational methods. However, the annotation process is more complicated in Eukaryotes; we used a comparative study for gene prediction using the FgenesH algorithm by various software providers. The final annotation of Aspergillus niger CBS 513.88. has been created as a GB file in Artemis, A sequence viewer and annotation tool was developed in the anger Institute

SpBase: the sea urchin genome database and web site

SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided

The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community