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.
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.
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.
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.
- 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.
- 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:
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). 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. 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 of these methods). 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.
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
|Relevant GO terms
|Return to AspGD||Send a Message to the AspGD Curators|
AspGD Copyright © 2008-2013 The Board of Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD.