1 July 2003
This page presents answers to some basic questions that new users might ask about SGD. An overview of information about the SGD website can be found on the Help Resources page.Contents:
SGD is an organized collection of genetic and molecular biological information about Saccharomyces cerevisiae, bakers' and brewers' yeast. It contains the sequences of yeast genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; links to literature information; links to functional genomics datasets; and tools for analysis and comparison of sequences. The SGD Home page is the main entry point for the database.
SGD is aimed at scientists; collected information about yeast for the non-scientist can be found at the Yeast Virtual Library. SGD does not collect medical information, and SGD curators cannot answer health-related questions.
An overview of the content and organization of SGD is presented in the sitemap.
The basic unit of SGD is the Locus Page (for an example, see ACT1). Each yeast gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to a DNA sequence, and chromosomal features (for example, centromeres) also have Locus Pages. All information relevant to a particular locus is either presented on or linked to the Locus Page. Tools for analysis and comparison of the locus are also accessible from the Locus Page.
Locus pages are accessible by using the Full Search form or by using the Search box at the top of any SGD Locus or tool page. In addition, gene or protein names appearing anywhere in SGD are hyperlinked to the corresponding Locus Page.
Many other SGD pages, including tools, documentation, data submission forms, and others, are accessible from the SGD Home page.
If you know the genetic or systematic name of the gene you are interested in, entering it in either the Search box at the top of most SGD pages or in the Full Search form will bring you to that Locus Page (or to a list of genes, if the same name has been used for two or more).
Sometimes you may need to investigate genes or proteins without knowing their names. You can search for a class of similarly named genes using the wildcard character (e.g., searching for 'pet*' brings up PET54, PET122, PET494...). Or, you can search with the name of a protein (e.g., profilin) or protein complex (e.g., cytochrome c oxidase), or a Gene Ontology term (see next section) to bring up lists of the Locus Pages where this text occurs. Each gene name in the hit list resulting from the search is hyperlinked to the corresponding Locus Page.
The Locus Page is the central clearinghouse for all information specific to that gene and tools for its analysis, including:
Gene products in SGD are classified according to the Gene Ontology (GO) system of classification. Each gene product is assigned GO terms that describe its molecular function and subcellular location, and the biological process in which it is involved. The terms may be searched to find the set of proteins that have been annotated to a particular term. A detailed explanation of the GO system and how to use and search it is presented in an SGD tutorial.
Lists of S. cerevisiae open reading frames and their characteristics are essential for keeping track of the results of any large-scale experiment. A variety of different tab-delimited text files containing data collected by SGD, listed in the data download directory of the SGD anonymous ftp site, are freely available for downloading.
Interpreting the results of functional genomics experiments that identify large groups of genes with something in common (e.g., transcriptional coregulation, similar null phenotypes, etc.) presents a special challenge in integrating what is known about each gene to find the significance of the trends observed. Two tools at SGD facilitate such analysis. The GO Slim Term Mapper takes a list of genes and displays how many are annotated to each of the parent GO Slim terms, allowing visualization of the distribution of the input gene set over broad biological processes, biochemical functions, or subcellular localizations. The GO Term Finder tool also takes a list of genes as input, and identifies GO terms shared among members of the group. The difference between the two tools is that the GO Slim Term Mapper maps genes to broad parent GO terms, while the Term Finder identifies specific, granular terms shared by the group. The GO tutorial provides details on the use of these tools.
The Gene/Sequence Resources page presents a versatile array of tools allowing retrieval and analysis of any portion of the S. cerevisiae genome, or analysis of your own input sequence. Sequences may be retrieved from a specific region of the genome, given a genetic name, systematic name, GenBank accession number, or clone name, and may include sequence upstream and/or downstream of the region if desired. Alternatively, chromosomal coordinates may be specified to retrieve part or all of a chromosome. Finally, the user may start with his/her own input sequence. Once a sequence is retrieved or entered, tools allow its analysis in multiple different ways, including translation, restriction mapping, BLAST and FASTA analysis, and primer design. The user may select a desired format (GCG, FASTA, etc.) for the output of many of the tools. The oligonucleotide primer design and BLAST analysis tools are also available as direct links from the toolbar at the top of many SGD pages.
Additional tools and resources that facilitate sequence analysis and cloning include the Pattern Matching tool, which finds short sequences or sequence patterns in nucleotide or protein sequences, and VectorDB, a collection of sequences and information about cloning vectors.
The Comparison Resources pull-down menu on each Locus Page allows you to look for proteins similar to that S. cerevisiae protein in other Saccharomyces species, in Candida albicans, in Caenorhabditis elegans, and in mammals. The link to Global Gene Hunter on each Locus Page allows a search of the RCSB Protein Data Bank for proteins of known structure that are similar to the protein of the Locus Page. Links to these tools are also found on the Homology and Comparisons page.
The Literature Guide linked to each Locus Page provides a list of papers curated by SGD that refer to similar genes and proteins in other species. For an example, see the list of papers in the topic "Non-Fungal Related Genes/Proteins" for ADE2.
The Analysis & Tools page is the starting point for several different genome-wide views. The Gene/Sequence Resources page allows you to select any stretch of DNA or an entire chromosome and to generate graphic representations or tables of the features present, with physical and/or genetic data. The Pairwise Chromosome Similarity View tool aligns selected chromosomes and displays sequence similarity matrices. A graphic Genomic view and physical and genetic maps of each chromosome are also available.
By consensus of the research community, SGD serves as the official arbiter of S. cerevisiae genetic nomenclature and maintains a gene name registry for new proposed gene names.
SGD also maintains the most up-to-date version of the complete genomic sequence of S. cerevisiae strain S288C. Updates to the sequence may be submitted to SGD from the research community; contact SGD curators for further information.
All of SGD's data are freely available to the public for download. SGD curators are available to assist researchers by creating custom files containing particular data of interest.
The SGD anonymous ftp site contains files of all SGD data and instructions for downloading them. The most commonly used data files are collected in the data download directory.
Several different kinds of information for the yeast community are available through SGD. You can add your contact information to SGD's directory of yeast colleagues, which can be searched by last name. You can also search or browse a list of more than 600 yeast labs. SGD maintains a list of upcoming conferences.
Current information about changes to SGD and news for the S. cerevisiae community is displayed on the SGD Home page; this information is also archived.
All SGD help resources are listed on the Help Resources page. The 'Help' button in the upper right corner of each tool and Locus page is linked directly to help documentation for that particular page.
For more general questions, the Frequently Asked Questions page is a good place to start. It includes common questions from SGD users about SGD and about S. cerevisiae and the genome sequence.
The Glossary page lists definitions of genetic, bioinformatic, and other terms used in SGD.
Tutorials for available to illustrate the use of some SGD tools.
A tutorial from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.SGD curators may be contacted by using a web form, by direct email to yeast-curator@genome.stanford.edu, or by fax at (650) 723-7016. We welcome comments and questions from the yeast community!
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