AspGD Help: Search AspGD


Contents:



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 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.

  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 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

  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 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

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 AspGD Restriction Analysis tool is available at AspGD Help: AspGD Genome Restriction Analysis.


Search Orthologs and Best Hits

Search AspGD Web Pages


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.

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