SGD Help: Global Gene Hunter

Contents


Description

The Global Gene Hunter allows the user to simultaneously search one or more of six 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.

Using Global Gene Hunter

  1. Selecting a Set of Databases to Search: Currently, six different databases can be searched using Global Gene Hunter. One, several, or all of the databases may be searched in any combination. In order to choose the databases you would like to search, click the gray button(s) next to the name(s) of the desired database(s). By default, all six databases are searched.

  2. Entering a Gene Name: One gene name may be searched by Global Gene Hunter at a time. Type the gene name into the box in the middle of the form labeled "Enter a gene or ORF name". The wildcard character (*) can be used at the end and/or beginning of the gene name. Please note that the wildcard character is not recognized by all databases for all searches and is sometimes ignored in the query.

    In addition to searching with the gene name entered, Global Gene Hunter will add the systematic name and any aliases of that gene to search criteria when the box labeled "Add gene name aliases to PubMed and Entrez Nucleotide search criteria" is selected. This will result in a search using all the gene name synonyms (Aliases) that are currently known to SGD.

    It is also possible to constrain the search results to S. cerevisiae-related information by clicking the box labeled "Narrow results to information regarding only Saccharomyces cerevisiae genes". Selecting this option does the following:

    After typing in the desired gene name, click the button labeled "Submit" to begin the search.

  3. Description of the Databases and How They Are Queried: The six databases which can currently be searched using Global Gene Hunter are listed below. Included is a brief description of each database and how it is queried by Global Gene Hunter.

    A. Saccharomyces Genome Database

    Description: 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 (Stanford).

    Query by Global Gene Hunter: Global Gene Hunter searches SGD for the gene name entered. The query retrieves the desired gene's Locus page, which contains information about its gene product, mutant phenotypes, location on the genetic map and physical map, DNA sequences, aliases and associated literature (Gene_info).

    B. PubMed (NCBI)

    Description: PubMed, a service of the National Library of Medicine, includes over 15 million citations for biomedical articles back to the 1950's. These citations are from MEDLINE and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources.

    Query by Global Gene Hunter: The Global Gene Hunter searches PubMed for all citations that include the selected gene name or gene product name in any field. When the search is constrained to information regarding only Saccharomyces cerevisiae genes, Global Gene Hunter searches PubMed for all citations that include the selected gene name or gene product name in any field and Saccharomyces cerevisiae in any field.

    C. Entrez Nucleotide (NCBI)

    Description: Managed by NCBI, the Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, EMBL, and DDBJ, the members of the tripartite, international collaboration of sequence databases. EMBL is the European Molecular Biology Laboratory at Hinxton Hall, UK; DDBJ is the DNA Database of Japan in Mishima, Japan. Sequence data are also incorporated from the Genome Sequence Data Base (GSDB), Santa Fe, NM. Patent sequences are incorporated through arrangements with the U.S. Patent and Trademark Office (USPTO) and via the collaborating international databases from other international patent offices.

    Query by Global Gene Hunter: The Global Gene Hunter queries Entrez Nucleotide for all sequences which include the entered gene name in the definition, comment, gene name, or gene description fields. When the search is constrained to information regarding only Saccharomyces cerevisiae genes, Global Gene Hunter queries Entrez Nucleotide for all sequences which include the entered gene name in the definition, comment, gene name, or gene description fields, and Saccharomyces cerevisiae in the organism field.

    D. Protein Data Bank (PDB) Homologs (Stanford)

    Description: Contains links to structural information in the RCSB Protein Data Bank (PDB) for S. cerevisiae proteins and for proteins of other species that have been determined, using Smith-Waterman analysis, to be similar to S. cerevisiae proteins.

    Query by Global Gene Hunter: The Global Gene Hunter searches PDB for the query gene or ORF name and for similar proteins in other species, and presents links to structural and alignment information.


    E. UniProt

    Description: The UniProt Consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Georgetown University Medical Center in Washington, DC, USA, is heir to the oldest protein sequence database, Margaret Dayhoff's Atlas of Protein Sequence and Structure. In 2002, EBI, SIB, and PIR joined forces as the UniProt Consortium. UniProt provides annotations such as the "description of the function of a protein, its domains and structure, post-translational modifications, variants, etc."

    Query by Global Gene Hunter: The Global Gene Hunter searches UniProt for all protein sequences that include the selected gene name in any field. When the search is constrained to information regarding only Saccharomyces cerevisiae genes, Global Gene Hunter queries UniProt for all protein sequences that include the selected gene name in any field and Saccharomyces cerevisiae in the organism field.

    F. Comprehensive Yeast Genome Database (MIPS)

    Description: The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.

    Query by Global Gene Hunter: Global Gene Hunter queries CYGD for the selected gene name.

Accessing Global Gene Hunter

Global Gene Hunter can be accessed either by (1) selecting "Full Search" from the menu bar at the top of most SGD web pages, then selecting "Global Gene Hunter" from the Specialized Gene and Sequence Searches section at the bottom of the Search Options page, or (2) by clicking on the "Global Gene Hunter" link at the top left of the SGD homepage under Search Options.

Other Relevant Links

  1. Links within SGD
    1. Search SGD
    2. Gene/Sequence Resources
    3. PDB Homolog Query
  2. External links
    1. PubMed
    2. GenBank
    3. RCSB Protein Databank (PDB)
    4. SWISS-PROT

Associated Glossary Terms:

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