CGD Help: Advanced Search

Contents:

Overview

Using the Advanced Search query form (building your search)

Choosing the chromosomal features (required Step 1)

Refining your search (optional Step 2)

Results page

Manage gene lists

Other searches available at CGD

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 CGD 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 Candida albicans chromosome X, choose Candida albicans 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

In Step 1, you must select at least one chromosomal feature type by clicking on the relevant checkbox (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 CGD is assigned a "Feature Type". This information is located on the locus page, immediately below the systematic name. The "not physically mapped" feature type is specially defined as features that are not mapped to a specific chromosomal location in CGD (e.g., genes that have been defined genetically but not cloned, or genes for which sequence information is not published).

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 CGD. You can also narrow your results by choosing one or more search criteria in Step 3.

Refining your search

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:

Feature Qualifiers
Selecting a checkbox narrows the results to feature types that have been assigned the qualifier. ORFs that are present in the current sequence assembly (not deleted ORFs) are assigned the additional qualifiers, Verified or Uncharacterized; selection of one or more of these qualifiers may be used to limit an ORF search. ORFs are labeled as Verified if there is experimental characterization that indicates that a functional gene product is produced (as defined by the ORF having curated Gene Ontology terms with experimental evidence codes, i.e., evidence codes other than IEA, ISS, RCA, ISA, ISM, ISO, NAS). Uncharacterized ORFs do not currently have curated experimental characterization. Upon publication that provides experimental evidence that an Uncharacterized ORF produces a product, the ORF will be reclassified as Verified. An additional qualifier, "Dubious," is in use for C. albicans ORFs. Dubious ORFs are unlikely to encode a protein product, as they appear indistinguishable from random non-coding sequence based on comparative analysis conducted by Lin et al. (2008), they show no significant homology to an S. cerevisiae gene (by the same criteria used to determine Best Hits and Orthologs at CGD), and they have no experimental characterization.

Introns and UTRs
Selecting "Yes" narrows the results to features that contain an intron, have annotated UTR(s), or have UTR intron(s). Selecting "No" narrows the results to those that do not contain intronic or UTR sequence, as selected.

Chromosomal location
Selecting a chromosome number limits the results to the selected features types that are located on the specified chromosome. You may select more than one chromosome or deselect a chromosome by pressing the Control (PC) or Command (Mac) key while clicking. The default option includes selected features on all chromosomes.

Gene Ontology (GO) annotation:

GO-Slim
Selecting a GO-Slim term limits the results to the feature types with GO annotations that map to that GO-Slim term (i.e., you will retrieve features annotated directly to the GO terms you select as well as any children of those GO terms). If you select multiple GO terms, resulting features must be annotated to all terms you select (the search uses a logical Boolean "AND," not "OR"). You can select or deselect multiple GO terms by pressing Control [PC] or Command [Mac] while clicking. Note that in addition to the GO Slim terms provided in the Biological Process, Molecular Function, and Cellular Component boxes, you can enter your own GO terms of interest by entering them in the empty text box. The behavior of the search will be the same: features will be retrieved whether they are directly or indirectly annotated to the GO terms that you enter. You may also limit your query by GO evidence code or by annotation method (Computational, High-throughput, or Manually Curated GO Annotations; see the SGD glossary for more detailed definitions). Please note that the search places a logical "OR" between the selected annotation methods and between the selected evidence code options, whereas the search places a logical "AND" between selected GO terms.

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 "Manage your gene list". This allows you to directly import the results into the GO Term Finder or the GO Slim Mapper to do further analysis, or to view a Summary of GO annotations. You will also be able to sort the list alphabetically by systematic name or by gene name. In addition, you will be able to download your results directly as a text file.