AspGD Help: Search AspGD

Contents:

AspGD Search Overview AspGD Basic Searches AspGD Advanced Searches Specialized Gene and Sequence Searches Orthologs and Best Hits Search AspGD Web Pages Search Aspergillus Literature Search for Colleagues

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

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.

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.

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