SGD

SGD Help: Search SGD

Contents:


SGD Search Overview

Searches at SGD provide access to information stored in the database. This help page gives you an overview of the searches available at SGD, along with detailed descriptions of the types of search parameters associated with each of the searches.

SGD Basic Searches

Both the Quick Search and the Category Search are case insensitive and support wildcard searches. The wildcard character (*) can be used in the beginning and/or at the end of the term to be searched. Examples of searches are available.

  1. Quick Search

    The Quick Search is available in the toolbar located at the top of most pages. It is case insensitive and supports wildcard searches. Queries using the Quick Search option search a limited set of information in the database. The results of the quick search can include matches in the following categories:

    * Gene name (systematic ORF name, standard gene name, reserved gene name, or alias)
    * Gene product
    * Gene Ontology (GO) term (a term name or a synonym)
    * Gene Ontology (GO) ID
    * Colleague
    * Author of a reference stored at SGD
    * Biochemical pathway name
    * PubMed IDs
    * Gene product descriptions
    * External database identifiers (E.C. number or UniProt ID)

  2. Text Search

    The Text Search searches additional fields in the database. It is the best search option to perform a broad search based on your search criterion. Like the Quick Search it is case insensitive and supports wildcard searches. The results of the quick search can include matches in the following categories:

    * Gene name (systematic ORF name, standard gene name, reserved gene name, or alias)
    * Gene product
    * Gene Ontology (GO) term (a term name or a synonym)
    * Colleague
    * Author of a reference stored at SGD
    * Biochemical pathway name
    * Gene product descriptions
    * Gene summary paragraphs
    * Abstracts
    * Name descriptions
    * phenotypes
    * Locus History notes

SGD Advanced Searches

  1. Advanced Search
    This search allows one to find a chromosomal feature (e.g. gene, ORF, centromere) based on selected criteria (e.g. calculated pI, MW, chromosome number, GO-Slim terms, etc.). For more information on the Advanced Search, please see the SGD Help: Advanced Search

Search SGD Web Pages

This is a Google Search of the html pages for the site 'genome-www.stanford.edu.' To search, enter one or more keywords into the box and click "Seek." The results displayed are those of a Google search and include a list of html pages that contain all of the words typed in the search box. For more information on the Google Search, please see The Basics of Google Search. Please note that this search does not search the SGD relational database.

Search Yeast Literature

  1. Search SGD Literature Guide
    Type in a gene name, reserved gene name, alias, or ORF name to go to the Literature Guide, featuring SGD curated papers, for the gene or ORF. The search is case insensitive and supports the wildcard character (*). If there is only 1 match to your search criterion, you will be immediately redirected to the literature guide page for that gene or ORF. If there is more than 1 match, the results will be a list of genes or ORFs. Each gene or ORF name is a link to the literature guide.

  2. View list of Genome-Wide Analysis Papers in SGD
    This link takes you to all SGD curated papers that have been associated with the Literature Guide topic "Genome-Wide Analysis." For a description of the "Genome-Wide Analysis" topic and general help on the SGD Literature Guide feature, please view SGD Help: Literature Guide

  3. Table of Gene Summary Paragraphs
    Links to a table listing all the genes which currently have Gene Summary Paragraphs (summaries of published biological information for a gene and its product that are written by SGD curators).

  4. Yeast Genome Directory
    This link goes directly to the Yeast Genome Directory published in Nature (vol. 387, May 29, 1997). The directory includes an introduction, maps, and letters to Nature regarding the nucleotide sequences of several chromosomes.

  5. YGMB Meeting Abstracts
    You can search abstracts from previous YGMB meetings by clicking on a highlighted year. The electronic abstracts are stored at SGD and searched using Webglimpse software.

Specialized Gene and Sequence Searches

  1. Chromosome History Search
    Displays the complete sequence and annotation history of each chromosome since the initial release of the systematic reference sequence in 1996. Select a chromosome from the pull-down list.

  2. Global Gene Hunter
    The Global Gene Hunter allows the user to simultaneously search one or more of seven different databases for a given gene name. The user is able to select the set of databases to be queried. In this manner, the user can quickly find all information contained in specific databases for a given gene. For help on using this feature, see SGD Help: Global Gene Hunter

  3. Gene/Sequence Resources
    Gene/Sequence Resources allows one to retrieve a list of options for accessing information available for 1) a named gene or sequence, 2) a specified chromosomal region, or 3) a raw DNA or protein sequence. This information includes biological information, table/map displays, and sequence analysis and retrieval options. For specific help on this resource, see SGD Help: Gene/Sequence Resources.

  4. Search clones
    This query is restricted to searching for a clone that matches your search criterion. Any of the following can be the search criterion:
    * a 4 digit number to search for a WashU clone
    * a 5 digit number to search for an ATCC lambda or cosmid clone
    * the ORF name
    The clone search by ORF name supports a wild card search.

    Since the WashU and ATCC clones are unique, you will be immediately redirected to a page that displays the information for that clone. For clone searches using an ORF name, the result will be a map that visually displays all clones that contain part of or all of the ORF(s) used as your search criteria.

Search Gene Function Information

  1. Search Yeast Biochemical Pathways
    Search for reactions, pathways, and compounds used in metabolic pathways that occur in S. cerevisiae. For more specific help on this resource, please see the Pathway Tools Query Help.

  2. Function Junction
    Function Junction simultaneously searches a variety of functional analysis project sites for all available functional information for a given gene or ORF. For more specific help on this resource, please see SGD Help: Function Junction

  3. Expression Connection
    Expression Connection simultaneously searches the results of several microarray studies for gene expression data for a given gene or ORF. For more specific help on this resource, please see SGD Help: Expression Connection.

  4. Query SAGE data
    The Query SAGE resource allows one to query the 1997 SAGE data of Velculescu et al. ((1997) Cell 88:243-251) using either a Simply Query (search using Gene/ORF name or chromosomal region) or an Advanced Query (search using Gene/ORF name, tag sequence, or relative expression values). For more specific help on this resource, please see SGD Help: Querying SAGE Data

Search Protein Information

  1. Search Protein Info
    Find the protein info page for a given locus, searching by locus name, ORF name, or SGDID. The protein info page contains basic protein information calculated from the predicted sequence as well as links to a variety of secondary structure and tertiary structure resources.

  2. PDB Homology Query
    The PDB Homology Query allows you to search for structural information on S. cerevisiae proteins and their homologs. Search by gene/ORF name, keyword, PDB Identifier, or Chromosome number to retrieve a given yeast protein structure (if it has been solved) and other proteins of known structure, regardless of source, that have sequence similarity to the query protein.

  3. Yeast Protein Motif Query
    The Yeast Protein Motif Query allows one to identify motifs contained in a query protein and lists other yeast proteins that also contain those motifs.

Search Colleague Information

  1. Search SGD Colleagues
    The query will be restricted to searching the last names of the colleagues who have submitted information to the database. Since the information is searched EXACTLY how it is entered in the database, a wildcard search is especially useful here.

    If there is only 1 match to your search criterion, you will be imediately redirected to the colleague page. If there is more than 1 match, the results will be displayed in a table that contains the following information: colleague name, the organization, and basic contact information such as phone number, fax number, and email address. The colleague name is a link to the full colleague information.

  2. Yeast Laboratories
    The Yeast Laboratories page provides a list of yeast research laboratories and displays contact information, links to web pages, gene names and keywords as provided by yeast colleagues.

Other Searches available at SGD

Associated glossary terms

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