DNA/Clone search and results
- Leonore Reiser
Using the DNA Search
The DNA Search provides three ways of searching for DNA resources:A simple search by name only, complex search using more limits, and search by position. These are offered in three distinct sections of the window. Depending upon the TYPE of DNA you search for different feature parameters will be displayed. If you are looking for stocks (including libraries, antibodies etc... please try the ABRC or RIKEN stock centers.
Search for
The drop down menu allows you to choose they type of DNA to search. The following table lists the types of DNA you can retrieve with this search along with their definitions. For help with feature parameters for specific DNA types, click the corresponding link to show feartures.
| DNA Type | Definition | Feature Parameters |
| clone | A section of DNA that has been inserted into a vector molecule, such as a plasmid or a phage or yeast chromosome, and then replicated to form many identical copies. | show features |
| vector | In DNA cloning, the plasmid or phage chromosome used to carry the cloned DNA segment. Also refers to the plasmids used to transform a plant. | show features |
Search by Name
Depending on the type of DNA you are searching for you can search with up to three of the following names/descriptions. Each name/description will be treated as a logical and. For example, a search for clone name =pROC + donor name = Ecker will find all clones named pROC that were donated by Joe Ecker.
| Option | Definition | for which DNA type | Name help |
| clone name | the name of the clone | clone | Help |
| gene name | name of the gene associated to the clone | clone | |
| clone end name | name of the clone end | clone, | |
| locus name | chromosome based name for genomic sequence corresponding to a transcribed unit | clone | Help |
| GenBank Accession | unique identifier for a sequence entry in GenBank | clone | Help |
| Vector Name | name of the vector | vector |
Features
The Restrict by Features options are below the Search by Name options on the DNA Search window. All the options in this section are an 'AND' operation. If the name input box is left blank, the software searches all the entries in the database matching the selected criteria.The following features are available for searching. Note not all features are available for all types of searches.
Vector type
Use this field to limit your search to one or more types of cloning vector. To select multiple vectors: select and press the APPLE key +mouse click (MAC) or press CTRL+ mouse click (PC). Choosing any will include all types of vectors in the results.
Used for clone, clone end, libary and vector searches.
Insert type
Use this field to limit your search to clones, clone ends, vectors and libraries containing specific types of DNA inserted into the cloning vector.To select multiple insert types: select and press the APPLE key +mouse click (MAC) or press CTRL+ mouse click (PC). Choosing any will include all insert types in the results.
Used for clone, clone end, vector and library searches.
Clone end type
Use this field to limit your search to clones and clone ends having a specific type of end.To select types: select and press the APPLE key +mouse click (MAC) or press CTRL+ mouse click (PC). Choosing any will include all types in the results.
Used for clone and clone end searches
Other features
Use these parameters to limit your search to include one or more of these features. To select multiple: select and press the APPLE key +mouse click (MAC) or press CTRL+ mouse click (PC).
| Feature | Usage | Available searches |
|---|---|---|
| is sequenced | Restrict the search to only entries with sequence data.For example, to find an EST or BAC clone with sequence. | clone, clone end |
| is genetic marker | Restrict your search to clones and clone ends that are genetic markers. For example to find clones used as RFLP markers. | clone, clone end |
| is on a map | Restrict your search to clones and clone ends that have been placed on a sequence, genetic or physical map. | clone, clone end |
| is full length cDNA | Restrict your search to include only clones that contain full length cDNAs. | clone |
Restrict by Map Location
This section lets you restrict your search by location on the reference genome map.
Chromosome
Lets you limit your search to a single chromosome. There are five nuclear chromosomes in Arabidopsis: 1, 2, 3, 4, and 5. You can also search the chloroplast and mitochondrial genomes.
Range
Lets you specify a range search by the upper and lower bounds on the reference genome. The value is interpreted based on the selected in kilobase pairs.