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The Advanced Search allows you to easily 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 SGD as well as detailed descriptions of the search criteria that can be used to limit your results.In the 1st step of the search, you choose the types of chromosomal features that you want to retrieve, and you can use the 2nd step of the search to narrow your results. If, for example, you want to retrieve all the tRNAs in the yeast genome, check the tRNA box in Step 1 and click on the Search button. If you want all the tRNAs found on chromosome X, check the tRNA box in Step 1, then in Step 2, select "X" from the Chromosome pulldown in the Annotation/sequence properties section. The sections below describe the required and optional criteria in more detail.
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 SGD is assigned a "Feature Type". This information is located on the locus page, immediately below the systematic name. Also included are some specially defined feature types in SGD:
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 SGD. You can also narrow your results by choosing one or more search criteria in Step 2.
In Step 2, 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 a search criteria blank generally means that it 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 include Dubious, Uncharacterized, and Verified features, but not Merged or Deleted ones.
Annotation/sequence properties:
- Feature qualifiers (e.g. Dubious, Uncharacterized)
Selecting any of these boxes will narrow your results by retrieving chromosomal features that are associated with your qualifier of choice. Note that by default (i.e. when no boxes are chosen), your results include Dubious, Uncharacterized, and Verified features, but not Merged or Deleted ones. See Associated glossary terms for details on these qualifiers.- Introns
Selecting "Yes" narrows the results to feature types that contain an intron. Selecting "No" narrows the results to those that do not contain an intron.- Frameshift translation
Selecting "Yes" narrows the results to feature types that contain a frameshift translation. Selecting "No" narrows the results to those that do not contain an frameshift translation.- 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.Protein properties:
Molecular weight
This can be used to find ORFs that encode for proteins between a defined range of molecular weights. Positive numbers must be entered in daltons in both dialog boxes. To find proteins smaller than a certain molecular weight, use 1 as the lower limit. To find proteins larger than a certain molecular weight, use any very large number as the upper limit. These numbers were caluclated using PeptideSort from GCG.Protein length
This can be used to find ORFs that encode for proteins with amino acid length that fall between a specified range. Positive numbers must be entered in both dialog boxes. To find proteins smaller than a certain protein length, use 1 as the lower limit. To find proteins larger than a certain protein length, use any very large number as the upper limit.pI (calculated)
This can be used to find ORFs that encode for proteins between a defined range of isoelectric points. Positive numbers must be entered in both dialog boxes. To find proteins smaller than a certain isoeletric point, use 1 as the lower limit. To find proteins larger than a certain isoelectric point, use any very large number as the upper limit. These numbers were calculated using PeptideSort from GCG.Phenotype properties:
- Systematic deletion phenotype
Selecting "Inviable" narrows the results to feature types that were determined inviable by the systematic deletion project. Select "Viable" narrows the results to those that were determined to be viable by the systematic deletion project. You should choose only one of these options. Although there are other systmatic deletion studies, these are not included in the search criteria at this time.Interaction properties:
- Has a physical interaction
Selecting "yes" narrows the results to features that have physical interaction data in SGD.- Exhibits a genetic interaction
Selecting "yes" narrows the results to features that have genetic interaction data in SGD.- Note on interaction data: Interaction data are not complete or exhaustive, so choosing "No" for either of these options is really looking for genes that have no interaction data available in SGD, not genes that are known to exhibit a particular interaction. Selecting "No" for both options will return features that have no interaction data in SGD.
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 (i.e. the search uses AND not OR). Yon 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. Note that 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.Large-scale expression:
- Features whose expression...
This option allows you to limit your search based on the levels of expression of your selected features in any of the Expression Connection data sets. Choose a particular expression behavior in the pulldown menu and enter a number to indicate the level of expression (must be an integer greater than or equal to 2).
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: Feature Qualifier | Gene Name | Description | Molecular Weight (if searched) |
Protein Length (if searched) |
pI (if searched) |
Position info (if searched) |
Phenotype (if searched) |
Genetic Interactions (if searched) |
Physical Interactions (if searched) |
Relevant GO terms (if searched) |
Relevant Expression Datasets (if searched) |
|---|
Keyword searches can be performed using the Quick Search box or the Category Search, both located on the Search Options Contents page. The Quick Search box is also located at the top of most SGD pages.
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