Saccharomyces Genome Database
Model Organism Database | |
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Licence | Free |
Website | http://www.yeastgenome.org |
The Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.[1] Further information is located at the Yeastract curated repository.[2]
Saccharomyces Genome Database
The SGD provides Internet access to the complete Saccharomyces cerevisiae genomic
Information collection
SGD keep reference genome sequence for the budding yeast S.cerevisiae. SGD are the source of the genome sequence for S. cerevisiae S288C strain background, includes catalog of genes and chromosomal feature of genome.
One of important function of SGD is biocuration of the yeast literature. SGD biocurators search all the scientific literature that relevant to S. cerevisiae, read the papers and capture their major finding in various defined fields of the database.[3]
The biocurators at SGD aim to annotate each gene by identifying function(s) from primary literature and linking to terms using the structured knowledge representation in the
Biochemical pathways are manually curated by SGD and provided using the Pathway Tools browser version 15.0 (13). The SGD biochemical pathways data set for S. cerevisiae, one of the most highly curated data sets among all Pathway Tools data sets available, is the gold standard for budding yeast; SGD supports an ongoing effort to update and enhance these data. The Pathway Tools interface provides a complete description of each pathway, with molecular structures, E.C. numbers and full reference listing. The updated pathways browser provides several enhanced features, including download of a list of genes found in a pathway for further analysis with other tools available at SGD. The pathway browser is hyperlinked via the ‘Pathways’ section of the Locus Summary page. The Pathway display is available from http://pathway.yeastgenome.org.[3]
Nomenclature
SGD continues to maintain the S. cerevisiae genomic nomenclature. The job is to promote the community-defined nomenclature standards and to ensure that the agreed-upon guidelines are followed in naming new genes or assigning new names to previously identified genes. Community guidelines state that the first published name for a gene becomes the standard name. However, prior to publication, a gene name may be registered and displayed in SGD in order to notify the community of its intended use. If there are disagreements or naming conflicts, we communicate with the relevant researchers within the community and negotiate an agreement whenever possible. The majority of those working on the gene in question must agree to any nomenclature change before it is implemented in SGD. In addition to maintaining genetic names, SGD ensures that the names of ORFs, ARS elements, tRNAs and other chromosomal features also conform to agreed-upon formats. Over the past two years 154 new gene names have been assigned and 21 community-initiated name changes have been processed.[3]
Analysis methods
There are several different analysis tools provided by SGD.
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BLAST, Basic Local Alignment Search Tool, the program is designed to find similar regions between biological sequences. SGD allows users to run BLAST searches of S. cerevisiae sequence datasets.
Fungal BLAST allows searches between multiple fungal sequences
Gene Ontology (GO) Term Finder searches for significant shared GO terms or their parents, and is used to describe the genes queried to help users discover what the gene have in common.
GO Slim Mapper maps annotations of a group of genes to more general terms and/or bins them into broad categories.
Pattern Matching is a resource that allows users to search for short nucleotide or peptide sequences of less than 20 residues, or ambiguous/degenerate patterns.
Restriction Analysis allows users to perform a restriction analysis by entering a sequence name or arbitrary DNA sequence[6]
References
External links
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