AspGD Help: Search AspGD

Contents:

AspGD Search Overview AspGD Basic Searches AspGD Advanced Searches Specialized Gene and Sequence Searches S. cerevisiae Orthologs and Best Hits Search AspGD Web Pages Search Aspergillus Literature Search for Colleagues Associated glossary terms

AspGD Search Overview

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.

AspGD Basic Searches

Both the Quick Search and the Category 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.

1. Quick Search
   

   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 S. cerevisiae ortholog or Best Hit

   * 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

   
   
2. Text Search
   

   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 S. cerevisiae ortholog or Best Hit

   * 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

   
   

AspGD Advanced Searches

1. Advanced Search
   This search allows one to find a chromosomal feature (e.g. gene, ORF, centromere) based on selected criteria (e.g. feature type, annotation/sequence properties, chromosome number, GO-Slim terms, etc.). For more information on the Advanced Search, please see the AspGD Help: Advanced Search.

2. Batch Download
   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.

3. Expanded Phenotype Search
   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.

Specialized Gene and Sequence Searches

1. Gene/Sequence Resources (Get Sequence)
   Gene/Sequence Resources allows one to retrieve a list of options for accessing information available for 1) a named gene or sequence, 2) a specified chromosomal region, or 3) a raw DNA or protein sequence. This information includes biological information, table/map displays, and sequence analysis and retrieval options. For specific help on this resource, see AspGD Help: Gene/Sequence Resources.

2. BLAST
   This tool allows comparing any DNA or protein sequence against several Aspergillus datasets. For more information on the BLAST resource, please see AspGD Help: BLAST Searches.

3. GBrowse Genome Browser
   GBrowse is a genome visualization tool that allows one to view and navigate genomic sequence. For more specific help about GBrowse, please visit the GBrowse Help.

4. Pattern Matching
   This tool allows searching for short (<20 residues) nucleotide or peptide sequences, or peptide sequences, or ambiguous/degenerate patterns. It uses the same datasets as AspGD BLAST. More specific information on this resource is available at AspGD Help: Pattern Matching.

5. Design Primer
   The tool helps in designing sequencing or PCR primers based on Aspergillus sequences. More help on how to use Web Primer is available at the Using Web Primer help pages.

6. Restriction Analysis
   This tool can be used to generate a restriction map of a DNA sequence (either the gene name, or ORF name, or an actual DNA sequence, can be given. More information on the CGD Restriction Analysis tool is available at AspGD Help: AspGD Genome Restriction Analysis.

7. Global Gene Hunter
   The Global Gene Hunter allows the user to simultaneously search one or more of four 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. For help on using this feature, see AspGD Help: Global Gene Hunter.

Search S. cerevisiae Orthologs and Best Hits

You may enter the Standard Name of an S. cerevisiae gene or genes, and the tool will return the Aspergillus ortholog or Best Hit. The S. cerevisiae gene may also be entered in the AspGD Basic Searches. The wildcard character "*" may also be used in these searches; for example, a search on "CDC*" will return all Aspergillus orthologs of the S. cervevisiae CDC genes. Please note that the name entered must be the Standard Name of the S. cerevisiae gene as defined at the Saccharomyces Genome Database; other gene aliases will not be recognized. The ortholog mappings between Aspergillus and S. cerevisiae were generated using the InParanoid software, as described in more detail on the Locus page documentation. To identify homologs at lower stringency than that required by the strict ortholog mapping criteria, Aspergillus genes that lack S. cerevisiae orthologs were subject to BLASTp comparison with an expectation value (E) of 1e-5 against the set of S. cerevisiae ORF translations from SGD, and the resulting matches are designated Best Hits. The ortholog and Best Hit mapping files may also be downloaded in bulk from the CGD web site.

If there is only 1 match to your search criterion, you will be immediately redirected to the protein info page for that gene or ORF. If there is more than 1 match, the results will be displayed in a table with your search criterion highlighted in yellow.

Search AspGD Web Pages

This is a Google Search of the html pages for the site "http://www.aspergillusgenome.org/" To search, enter one or more keywords into the box and click "Seek." The results displayed are those of a Google search and include a list of html pages that contain all of the words typed in the search box. For more information on the Google Search, please see The Basics of Google Search. Please note that this search does not search the AspGD relational database.

Search Aspergillus Literature

1. Search AspGD Literature Guide
   Type in a gene name, reserved gene name, alias, or ORF name to go to the Literature Guide, featuring AspGD curated papers, for the gene or ORF. The search is case insensitive and supports the wildcard character (*). If there is only 1 match to your search criterion, you will be immediately redirected to the literature guide page for that gene or ORF. If there is more than 1 match, the results will be a list of genes or ORFs. Each gene or ORF name is a link to the literature guide.

2. List of Genome-Wide Analysis Papers
   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.

Search Colleague Information

1. Search AspGD Colleagues
   The query will be restricted to searching the last names of the colleagues who have submitted information to the database. Since the information is searched EXACTLY how it is entered in the database, a wildcard search is especially useful here.
   
   If there is only 1 match to your search criterion, you will be imediately redirected to the colleague page. If there is more than 1 match, the results will be displayed in a table that contains the following information: colleague name, the organization, and basic contact information such as phone number, fax number, and email address. The colleague name is a link to the full colleague information.
2. Aspergillus Laboratories
   The Aspergillus Laboratories page provides a list of Aspergillus research laboratories and displays contact information, links to web pages, gene names and keywords as provided by colleagues.

Associated glossary terms, provided by SGD

• Author
• Colleague
• Feature
• Genbank
• Gene name
• Gene Ontology (GO)
• Locus
• ORF
• AspGDID
• Text
• Wild card character
• See entire glossary

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