SGD Help: Global Gene Hunter

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.

Contents

1. Using Global Gene Hunter
2. Databases and Queries

Using Global Gene Hunter

1. Step 1: Select 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. Step 2: Enter 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.
3. Optional Step 3: Add aliases
   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.
4. Optional Step 4: limit to S. cerevisiae
   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:
• Adds the criterion "Saccharomyces cerevisiae[all]" to the PubMed query
• Adds the criterion "Saccharomyces cerevisiae[organism]" to the Entrez Nucleotide query
• Adds the criterion "Saccharomyces cerevisiae[organism]" to the UniProt query
5. Step 5: Submit
   Click the button labeled "Submit" to begin the search.

Databases and Queries

The six databases that are currently searched by Global Gene Hunter are listed below. Included is a brief description of each database and how it is queried by Global Gene Hunter.

• Saccharomyces Genome Database

  SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. Global Gene Hunter searches SGD for the gene name entered. The query retrieves the desired gene's Locus Summary page, which displays or links to various types of information about the gene.

• PubMed (NCBI)

  PubMed, a service of the National Library of Medicine, includes millions of citations for biomedical articles back to the 1950's. PubMed includes links to many sites providing full text articles and other related resources.

  The Global Gene Hunter searches PubMed for all citations that include the entered gene name in any field. When the search is constrained to information regarding only S. cerevisiae genes, Global Gene Hunter searches PubMed for all citations that include the entered gene name in any field and "Saccharomyces cerevisiae" in any field.

• Entrez Nucleotide (NCBI)

  Managed by NCBI, the Entrez Nucleotide database is a collection of genome, gene, and transcript sequence data from several sources, including GenBank, EMBL, and DDBJ.

  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.

• Protein Data Bank (PDB) Homologs (Stanford)

  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.

  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.

• UniProt

  The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.

  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.

• Comprehensive Yeast Genome Database (MIPS)

  The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the budding yeast Saccharomyces cerevisiae.

  Global Gene Hunter queries CYGD for the selected gene name.

Go to Global Gene Hunter