Contents:
Searches at AspGD provide access to information stored in the database.
This help page gives you an overview of the searches available at AspGD,
along with detailed descriptions of the types of search parameters
associated with each of the searches.
Both the Quick Search and the Text 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. Quick Search and Text Search results are displayed in sections organized by species. Results that are not species-specific (e.g., GO terms, colleagues, references) are listed in a separate section on the results page.
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, or alias)
- * Gene name of ortholog or Best Hit from S. cerevisiae or other Aspergillus species
- * Gene description
- * Gene Ontology (GO) term (a term name or a synonym)
- * Gene Ontology (GO) ID
- * Phenotypes
- * Locus Summary Notes
- * Colleague
- * Author of a reference stored at AspGD
- * PubMed IDs
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 Text Search can include matches in the following categories:
- * Gene name (systematic ORF name, standard gene name, or alias)
- * Gene name of ortholog or Best Hit from S. cerevisiae or other Aspergillus species
- * Gene description
- * Gene Ontology (GO) term (a term name or a synonym)
- * Gene Ontology (GO) ID
- * Phenotypes
- * Locus Summary Notes
- * Colleague
- * Author of a reference stored at AspGD
- * PubMed IDs
- * Abstracts
- * Name descriptions
- * Locus History notes
The tool allows simultaneous retrieval of DNA and Protein sequences
for a list of Standard gene names or Feature names. For more
information on the Batch Download
Tool, please see the AspGD
Help: Batch Data Download.
The tool searches the text of all of the information associated with the ohenotype curation, including alleles, experimental conditions, and notes, in addition to the basic description of the phenotype itself.
This tool allows searches for orthologs of AspGD genes by the name (gene name, systematic name, or alias) of the ortholog. You may enter a gene name (wildcards permitted) and the search will return any match to orthologs of A. nidulans or A. fumigatus genes (additional species will be included in the future). AspGD contains mappings of A. nidulans and A. fumigatus genes to their orthologs in other Aspergillus species and to orthologs in S. cerevisiae; both sets are queried by this tool.
Orthologs among the Aspergilli are computed using a Jaccard clustering approach. Orthologs between individual Aspergillus species and S. cerevisiae are computed using InParanoid software, and, for genes that do not have an S. cerevisiae ortholog, Best Hits are computed using BLASTP. The specific details of the mapping proceduers are described in the Ortholog and Best Hit documentation.
The Search results return two columns.
The first column contains the name of the gene that:
1. matched the query entered in the search box, and
2. has an ortholog in A. nidulans or A. fumigatus.
The second column contains the name of the A. nidulans or A. fumigatus gene(s) whose ortholog is listed in Column 1.
Please note, regarding specifics of the query and the results displayed: The query searches the standard name, systematic name, and alias names (if any) of the A. nidulans and A. fumigatus genes in the AspGD ortholog mappings. However, the search results display the standard and systematic name only; alias names are not displayed, so it is possible that the gene name that matched the query is an alias that is not shown on the results page. For orthologs in S. cerevisiae, only the Standard Name of the S. cerevisiae gene, as defined at the Saccharomyces Genome Database, is searched. For genes that do not have a Standard Name, the systematic name is searched. Other S. cerevisiae gene aliases will not be recognized by the query.
The ortholog and Best Hit mapping files may also be downloaded in bulk from the AspGDweb site.
If there is only one match to your search criterion, you will be
immediately redirected to the Locus Summary page for that gene or ORF.
If there is more than one match, the results will be displayed in a
table.
This link takes you to all AspGD 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 AspGD Literature Guide feature, please view AspGD
Help: Literature Guide.
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AspGD Copyright © 2008-2013 The Board of Trustees, Leland
Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD. |