dictyBase Help:dictyBase Search

dictyBase Help: dictyBase Search

Contents


Description

At the top of each page on the dictyBase server is a powerful Search Tool that can be used to find genes, gene products, GenBank accession numbers, Gene Ontology terms, colleagues, and authors. This help page gives tips to use the Search Box successfully.

 

Finding a Gene Page

Searching for a gene name or an alias will return the appropriate Gene Page, provided that the name entered exists. For example, the cAR1 receptor Locus Page will be returned if you enter the gene name, carA, or the alias cAR1 (case insensitive). When in doubt, the Wildcard (*) can be used. Searching for car* will return a list of genes, aliases, accession numbers, gene products, gene ontology terms, colleagues and authors that begin with "car". In this example, the search results are as follows:

  • Search Results for : car*

  • 4 Gene names (gene name/alias/ORF name)
  • 0 GenBank Accession Numbers
  • 9 Gene products
  • 247 Gene Ontology terms (GO terms, synonyms)
  • 6 Colleagues (by last name)
  • 28 Authors (by last name, first initial)

The link of interest can be followed. By selecting "Gene names (gene name/alias/ORF name)", a list of all the genes in dictyBase beginning with "car" will be displayed: carA, carB, carC, and carD. Following each of these links leads to the appropriate Locus Page.

It is also possible to search for a gene product name. For example "cAMP receptor" returns one gene product. Following that link leads to a table that shows all the genes that encode cAMP receptors, carA, carB, carC, and carD. Again, following each of these links leads to the respective Locus Page.

 

Finding a Gene Ontology Term

dictyBase also annotates each gene product to Gene Ontology (GO) terms. The example "cAMP receptor" also represents a GO term. Following that link returns a table that displays the GO term, which aspect of GO that terms relates to (Molecular Function, Biological Process, Cellular Component), and the genes that have been annotated to that term: carA, carB, carC, and carD.

 

Finding a Researcher

Searching for a researcher name returns two types of entries: Colleagues and Authors.

  • Colleagues are researchers that have entered their profile in our Colleague database (to find out how to enter your profile see: Colleague Update/New Entry). Following the "Colleagues" link on the front page leads to the Colleague display Page. Help on finding a Colleague is also available.

  • Authors includes all the authors of research papers curated in dictyBase. Following that link leads to a list of all papers in dictyBase by that author, with links to the dictyBase Paper, to the PubMed abstract and to the Full Text Paper when these are available.

 

Searching the dictyNews

dictyNews is a newsletter that provides abstracts of papers accepted for publication and is released every 1 - 2 weeks, depending on demand. The Newsletter Archive can be browsed. It is possible to include the Newsletter Archive in the search. In the case of the "cAMP receptor" search, in addition to gene products and GO terms, 60 NewsLetter items are returned. The results display hyperlinks that go directly to the appropriate NewsLetter issue.

Please note that Boolean operators (OR, AND, NOT) are supported when searching the Newsletter Archive. If two terms are entered, the Search Function will use the AND operator by default. For example, to find the abstracts submitted by the Firtel lab in 2003, search for "Firtel 2003" or Firtel AND 2003". Either query will return all the Newsletter issues where both "Firtel" and "2003" appear.

 

Additional Considerations

  • The Search Function of dictyBase is case-insensitive.

  • The Search Function of dictyBase looks for an exact match unless the wildcard character * is used. This means although cAR1 will return a result, cAR 1 will not due to the space. The same is true for hyphens and other characters. If in doubt about an exact name, use the wildcard character.

  • In general, dictyBase curators remove spaces, hyphens, and "Dd" from gene names and aliases. For example Ddras and Dd-ras should be searched simply as ras and will return the rasD locus.

  • Boolean operators (OR, AND, NOT) are supported when searching the Newsletter Archive but not when searching the dictyBase database.

 

Relevant dictyBase Help Documents

 

Relevant dictyBase Glossary Terms

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