dictyBase Help: Global Gene Hunter

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Contents

• Description
• Using Global Gene Hunter
• Accessing Global Gene Hunter
• Other Relevant Links
• Glossary Terms

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Description

The Global Gene Hunter allows the user to simultaneously search one or more of five 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: There are currently five different databases that can be searched using Global Gene Hunter. Global Gene Hunter can search one, several, or all of the databases at a time in any combination. In order to choose the databases you would like to search, click the button(s) next to the name(s) of the desired database(s). By default, all 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 at the bottom of the form labelled "Enter a gene or ORF name." If dictyBase is one of the databases being searched, the wildcard character (*) can be added at the end and/or beginning of the gene name, and it will be recognized when Global Gene Hunter searches. However, the wildcard character is not recognized by other databases and is ignored in the query.

   It is possible to use Global Gene Hunter to search for gene name aliases in dictyBase, GenBank and PubMed by clicking on the box labelled "Search dictyBase, GenBank and PubMed for aliases." This will result in a search using all the gene name synonyms (alias ) that are known to dictyBase.

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

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

   I. dictyBase
   
   
   

   Description: Contains information about the molecular biology and genetics of Dictyostelium.

   Query by Global Gene Hunter: Global Gene Hunter searches the dictyBase Locus class for the gene name entered. The locus class contains information, both internally- and externally-linked, about every characterized locus in D. discoideum. The query retrieves the information from the desired gene's Locus Page.

   II. GenBank (NCBI)
   
   
   

   Description: GenBank is the NIH annotated genetic sequence database of all publically available DNA sequences. Managed by NCBI, GenBank is part of the International Nucleotide Sequence Database Collaboration that also includes DDBJ and EMBL.

   Query by Global Gene Hunter: The Global Gene Hunter queries GenBank for all sequences which include the entered gene name in the definition, comment, gene name, or gene description fields, and Dictyostelium discoideum in the organism field.

   III. PubMed (NCBI)
   
   
   

   Description: PubMed is NLM's search tool to access Medline and pre-Medline citations.

   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 and Dictyostelium in any field.

   IV. Swiss-Prot (Geneva)
   
   
   

   Description: Swiss-Prot is an annotated protein sequence database which is part of the ExPASy World Wide Web molecular biology server of the Geneva University Hospital and the University of Geneva. It 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 Swiss-Prot for all protein sequences that include the selected gene name and Dictyostelium discoideum in the DE (description), GN (gene name) OS (organism species) and OG (organelle) lines.

   V. Protein Information Resources (PIR) - Georgetown
   
   
   

   Description: The Protein Information Resources (PIR) Database is a protein and nucleic acid sequence database maintained by the National Biomedical Research Foundation (NBRF).

   Query by Global Gene Hunter: Global Gene Hunter searches PIR for the selected gene name and the species Dictyostelium discoideum.

Accessing Global Gene Hunter

Global Gene Hunter can be accessed from any locus page.

Other Relevant Links

1. Links within dictyBase
   1. dictyBase Glossary
2. External links
   1. GenBank
   2. PubMed
   3. SWISS-PROT

Associated Glossary Terms:

• EMBL
• GenBank
• Gene Name
• Gene Product
• Locus
• Medline
• NCBI
• Alias
• Phenotype
• PubMed
• Standard Name
• Swiss-Prot

Go to Global Gene Hunter