dictyBase Help: Global Gene Hunter
Contents
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.
- 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.
- 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.
- 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.
Global Gene Hunter can be accessed from
any locus page.
- Links within dictyBase
-
dictyBase Glossary
- External links
- GenBank
- PubMed
- SWISS-PROT
Go to Global Gene
Hunter
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