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Maria C Costanzo

Publications and source records attributed to Maria C Costanzo.

9 recordsLinked to original sources
PubMed2006

Expanded protein information at SGD: new pages and proteome browser.

The recent explosion in protein data generated from both directed small-scale studies and large-scale proteomics efforts has greatly expanded the quantity of available protein information and has prompted the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations. In particular, we have expanded ongoing efforts to improve the integration of experimental information and sequence-based predictions and have redesigned the protein information web pages. A key feature of this redesign is the development of a GBrowse-derived interactive Proteome Browser customized to improve the visualization of sequence-based protein information. This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using several popular prediction algorithms. In addition, a physico-chemical properties page has been introduced to provide easy access to basic protein information. Improvements to the layout of the Protein Information page and integration of the Proteome Browser will facilitate the ongoing expansion of sequence-specific experimental information captured in SGD, including post-translational modifications and other user-defined annotations. Finally, SGD continues to improve upon the availability of genetic and physical interaction data in an ongoing collaboration with BioGRID by providing direct access to more than 82,000 manually-curated interactions.

Computer Graphics↗
PubMed2006

Sequence resources at the Candida Genome Database.

The Candida Genome Database (CGD, http://www.candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at http://www.candidagenome.org/ and CGD curators may be contacted by email at candida-curator@genome.stanford.edu.

Candida albicans↗
PubMed2006

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

Sequencing and annotation of the entire Saccharomyces cerevisiae genome has made it possible to gain a genome-wide perspective on yeast genes and gene products. To make this information available on an ongoing basis, the Saccharomyces Genome Database (SGD) (http://www.yeastgenome.org/) has created the Genome Snapshot (http://db.yeastgenome.org/cgi-bin/genomeSnapShot.pl). The Genome Snapshot summarizes the current state of knowledge about the genes and chromosomal features of S.cerevisiae. The information is organized into two categories: (i) number of each type of chromosomal feature annotated in the genome and (ii) number and distribution of genes annotated to Gene Ontology terms. Detailed lists are accessible through SGD's Advanced Search tool (http://db.yeastgenome.org/cgi-bin/search/featureSearch), and all the data presented on this page are available from the SGD ftp site (ftp://ftp.yeastgenome.org/yeast/).

Chromosomes, Fungal↗
PubMed2006

The Candida Genome Database: facilitating research on Candida albicans molecular biology.

The Candida Genome Database (CGD; http://www.candidagenome.org) is a resource for information about the Candida albicans genomic sequence and the molecular biology of its encoded gene products. CGD collects and organizes data from the biological literature concerning C. albicans, and provides tools for viewing, searching, analysing, and downloading these data. CGD also serves as an organizing centre for the C. albicans research community, providing a gene-name registry, contact information, and research community news. This article describes the information contained in CGD and how to access it, either from the perspective of a bench scientist interested in the function of one or a few genes, or from the perspective of a biologist or bioinformatician interpreting large-scale functional genomic datasets.

Alleles↗
PubMed2005

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.

The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research community that is interested in the molecular biology of this fungus. CGD curators are in the process of combing the scientific literature to collect all C.albicans gene names and aliases; to assign gene ontology terms that describe the molecular function, biological process, and subcellular localization of each gene product; to annotate mutant phenotypes; and to summarize the function and biological context of each gene product in free-text description lines. CGD also provides community resources, including a reservation system for gene names and a colleague registry through which Candida researchers can share contact information and research interests. CGD is publicly funded (by NIH grant R01 DE15873-01 from the NIDCR) and is freely available at http://www.candidagenome.org/.

Candida albicans↗
PubMed2005

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae. SGD has recently developed two new resources that facilitate nucleotide and protein sequence comparisons between S.cerevisiae and other organisms. The Fungal BLAST tool provides directed searches against all fungal nucleotide and protein sequences available from GenBank, divided into categories according to organism, status of completeness and annotation, and source. The Model Organism BLASTP Best Hits resource displays, for each S.cerevisiae protein, the single most similar protein from several model organisms and presents links to the database pages of those proteins, facilitating access to curated information about potential orthologs of yeast proteins.

Databases, Genetic↗
PubMed2004

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across groups of genes with common features and across different species. The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar proteins from any species whose sequences are contained in the non-redundant (nr) protein data set at NCBI. The Yeast Biochemical Pathways tool integrates groups of genes by their common roles in metabolism and displays the metabolic pathways in a graphical form. Finally, the Find Chromosomal Features search interface provides a versatile tool for querying multiple types of information in SGD.

Amino Acid Sequence↗
PubMed2004

Saccharomyces genome database: underlying principles and organisation.

A scientific database can be a powerful tool for biologists in an era where large-scale genomic analysis, combined with smaller-scale scientific results, provides new insights into the roles of genes and their products in the cell. However, the collection and assimilation of data is, in itself, not enough to make a database useful. The data must be incorporated into the database and presented to the user in an intuitive and biologically significant manner. Most importantly, this presentation must be driven by the user's point of view; that is, from a biological perspective. The success of a scientific database can therefore be measured by the response of its users - statistically, by usage numbers and, in a less quantifiable way, by its relationship with the community it serves and its ability to serve as a model for similar projects. Since its inception ten years ago, the Saccharomyces Genome Database (SGD) has seen a dramatic increase in its usage, has developed and maintained a positive working relationship with the yeast research community, and has served as a template for at least one other database. The success of SGD, as measured by these criteria, is due in large part to philosophies that have guided its mission and organisation since it was established in 1993. This paper aims to detail these philosophies and how they shape the organisation and presentation of the database.

Databases, Nucleic Acid↗