AspGD Help: Advanced Search


Contents:


Overview

The Advanced Search allows you to retrieve the chromosomal features (ORFs, tRNAs, etc) of your choice from the database through a web interface. In addition, you may refine your results by choosing several different criteria.

This help page gives you an overview of the Advanced Search available at AspGD as well as detailed descriptions of the search criteria that can be used to limit your results.

Using the Advanced Search query form (building your search)

In the 1st step of the search, you choose the strain (genome) to search. Then, in the 2nd step, you choose the types of chromosomal features that you want to retrieve. Finally, you can use the 3rd step of the search to narrow your results. If, for example, you want to retrieve all the tRNAs in the genome, check the tRNA box in Step 1 and click on the Search button. If you want all the tRNAs found on Aspergillus nidulans chromosome X, choose Aspergillus nidulans in Step 1, check the tRNA box in Step 2, then in Step 3, select "X" from the Chromosome pulldown in the Annotation/sequence properties section. The sections below describe the required and optional criteria in more detail.

Choosing the strain and chromosomal features (required)

In Step 1, you must select a strain from the pull-down menu, and in Step 2, you must select at least one chromosomal feature type from those currently available at AspGD by clicking on the relevant checkbox (both steps 1 and 2 are required). You can select more than one feature type. A chromosomal feature is a sequence feature on the chromosome, such as an ORF, a tRNA, a snRNA, CEN, or ARS. Each chromosomal feature at AspGD is assigned a "Feature Type". This information is located on the locus page, immediately below the systematic name.

If you only select "ORF" and then submit the query, you will get a list of all chromosomal features that have the feature type of "ORF" at AspGD. You can also narrow your results by choosing one or more search criteria in Step 3.

Refining your search (optional)

In Step 3, choose search criteria if you want to restrict the results (optional). Search criteria are selected by clicking on a checkbox, filling in numbers in a dialog box, or selecting a menu option. Select or unselect multiple options for Chromosomes and GO terms by pressing the Control (PC) or Command (Mac) key while clicking. The results will be those chromosomal features that meet ALL the criteria selected or entered in this section (i.e., this part of the search uses AND across the different search criteria, not OR).

Note on defaults (i.e. when none of the optional criteria are selected): Leaving any search criteria blank generally means that they will not be used in restricting the results, so for example, the default for the chromosomal location option is that selected features on all chromosomes will be included and the default for the GO-Slim term option is that all selected features will be included, regardless of its mapping to a GO-Slim term. There is one exception: for the feature qualifiers, by default, your results do not include Deleted features.

Annotation/sequence properties:

Gene Ontology (GO) annotation:

Results page

The results page will give you a summary of your search results. At the top, it will state the number of chromosomal features that match the search critieria. Immediately below, the chromosomal feature type(s) selected for the search along with the search criteria selected to narrow the search will be listed. The number listed in parentheses indicates the numbers of hits available when that criterion is applied. This can be used to determine which criterion was the most restrictive when no hits are returned.

A table will be displayed with the chromosomal features that match your search criteria. The table will have the following information:

Systematic Name Feature Type Gene Name Description Position info
(if searched)
Relevant GO terms
(if searched)

Only 30 hits will be shown per page. If there are more than 30 hits, the subsequent pages will be hyperlinked.
You will also be given a table of options to "Analyze your gene list". This allows you to directly import the results into the GO Term Finder or the GO Slim Mapper to do further GO-based analysis, to use the Batch Download tool for retrieval of other data types (including gene descriptions and aliases, phenotypes, orthologs, sequences) or to view a Summary of GO annotations. In addition, you will be able to download the search your results directly as a text file.

Associated glossary terms, provided by SGD




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