Polymorphism/Allele Search and Results
- Leonore Reiser
Using the Polymorphism/Allele Search
The TAIR Polymorphism/Allele Search window provides three ways of narrowing your search in three distinct sections of the window: specifying name,specifying features, and specifying map location. If you make a mistake, use the reset button to reset the parameters. Note that resetting will reset ALL of the search parameters (such as name, type and date restrictions).
Search by Name
At the top of the TAIR Polymorphism/Allele Search window are the Search by Name options.
This simple search is case insensitive and allows you to search for exact matches, names that start with, contain or end with your input string. You may specify the full name or symbol of the polymorphism/allele, the full name or symbol of the wild type gene, the locus name (i.e. AT2g54790), or the last name of the person or organization who submitted the polymorphism/allele. You may select two different types of criteria (i.e. name and submitter last name) that will be searched together. (see "Using Wildcards").
Restrict by Features
The Restrict by Features options are below the Search by Name options on the TAIR Polymorphism/Allele Search window.
These options let you perform more complex searches. You may select multiple options within each parameter by clicking on one selection and then clicking on additional ones while holding down either the CTRL key (PCs) or the Apple key (Mac).
Polymorphism Features
Checking the "has associated genetic markers" box allows you to select only those polymorphisms/alleles with detection methods associated to them. You may also limit your search to only those polymorphisms that are also alleles by ticking the appropriate button.
Polymorphism Type
In TAIR, a polymorphism/allele is defined as any genetic variation between two ecotypes or within one ecotype that can be assessed experimentally by sequencing, PCR amplification, restriction digest analysis or phenotypic inspection. You can search one or more polymorphism/allele types 
.To select more than one type of polymorphism, hold down the CTRL key (PC) or Apple (Mac) while clicking on the selection with the mouse. The default option, any, finds all polymorphisms regardless of type.
Insertion Type
Limit your selection by the insertion type . To select more than one type of insertion hold down the CTRL key (PC) or Apple (Mac) while clicking on the selection with the mouse. The default option any, does not restrict the search by insertion type.
Polymorphism Site
Limit your selection by the location in the gene/genome where the polymorphism occurs. The sites are:
| Polymorphism Site | Comment |
|---|---|
Any | |
exon | |
intron | |
splice junction | May be either 5' or 3' splice site. |
Inheritance
Limit your selection by the mode of inheritance. You can select only one mode of inheritance. The modes are:
| Inheritance mode | Comment | Reference |
|---|---|---|
Any | Returns all polymorphisms/alleles regardless of inheritance. | |
dominant | Allele that produces the same character whether present in the homozygous or heterozygous state. | Oxford Dictionary of Biochemistry and Molecular Biology |
incompletely dominant | (also semi-dominant) Allele combination that produces a separate phenotype in the heterozygous state from the dominant homozygote and the recessive homozygotephenotypes | |
recessive | Allele that lacks effect when accompanied in the same diploid by a dominant form of the same gene. | Oxford Dictionary of Biochemistry and Molecular Biology |
Polymorphic Between
The default (unselected) status is "Any", which means that ecotype information is ignored in the query.
Limit your selection to those that have known polymorphisms in specific ecotypes. For example, searching between Landsberg erecta (Ler) and any ecotype will return all polymorphism/alleles for which a polymorphism in Ler is known. A search for polymorphisms between Landsberg erecta (Ler) and Columbia (Col) will return those polymorphism/alleles for which polymorphisms are known for both ecotypes. The current selection of ecotypes that can be queried are:
| Symbol | Full Name |
|---|---|
Be | Bensheim |
C24 | C24 |
Co | Coimbra |
Col | Columbia |
Cvi | Cape Verde Islands |
En | Enkheim |
Ler | Landsberg erecta |
Nd | Niederzenz |
No | Nossen |
Po | Poppelsdorf |
RLD | Rld |
Ws | Wassilewskija |
A search for Col will return results for all accessions (e.g., Col-1 and Col-4 are treated as Columbia).
Time Restriction
You can restrict your search to only include polymorphism/alleles that have been added or updated in the specified time period.
Mutagen
Limit your selection by the type of mutagen used to induce the polymorphism. The mutagens are:
| Mutagen Name | Comment |
|---|---|
Any | returns all polymorphisms/alleles regardless of the mutagen used |
transposon insertion | |
T-DNA insertion | |
Agrobacterium transformation | Covers both seed and whole plant transformation. |
diepoxybutane (DEB) | |
ethylmethane sulfonate (EMS) | |
ethyl-nitrosourea (ENU) | |
gamma-rays | |
fast neutrons | |
nitrosomethyl urea (NMU) | also methylnitrosourea (MNU) |
tissue culture | |
X-rays | |
unknown |
Restrict by Map Location
This section lets you restrict your search by location. If you make a mistake and choose the wrong chromosome or map type, use the reset button to reset the parameters. Note that resetting will reset ALL of the search parameters (such as name, type and date restrictions).
The options in this section let you use three parameters to restrict your search: Chromosome, Map Type, and Range.
Chromosome
Lets you limit your search to a single chromosome. There are five chromosomes in Arabidopsis: 1, 2, 3, 4, and 5.
Map Type
Lets you search entities by their position on a particular map and can be used with or without setting Range parameters. The map choices are: AGI sequence map, Lister and Dean Recombinant Inbred (RI) map and Classical map.You can only choose one map type for each search- the acceptible units for selecting a Range will appear once a map has been selected. To search on multiple map types, use the TAIR Map Viewer.You can also search and view polymorphism/alleles down to the nucleotide level on the AGI sequence map using the SeqViewer.
Range
Lets you specify a range search by the upper and lower bounds (when you select "Between") or a center point (when you select "Around"). The value is interpreted based on the selected range units. You can specify the range by distance (cM), physical distance (kb), and by polymorphism/allele or gene names. When you select "Between" from the drop-down menu, your search will be within the range defined by two entities or positions on a particular map. When you select "Around" from the drop-down menu, your search will be the area +/-10 cM and/or +/- 100 kb from the specified entity or position. When you choose search around, the second value input and units options are disabled.
Output Options
This section allows you to specify the number of records to display on each results page for your query, and how you would like your results to be grouped.
number of records/page
You can choose to have 25,50,100 or 200 records displayed on each results page for your query.
sort by
Allows you to order your results by polymorphism/allele name,type or position. For ordering by position, you do not need to specify a chromosome, but a map type must be defined. The default map for ordering by position is the AGI sequence map (when no map type is specified). If you choose a chromosome and opt to have the output displayed by position, then you must choose from one of the available map types.