Region search
The process of searching for a region entails defining the region of interest by some means, querying the database, and receiving the results in a summary table. You can search for a region here.
After opening the Region Search console, the first step is to define the type of search you wish, using the left side of the console. There are four quick steps to this process.
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1)
Select the chromosome of interest from the pop-up 
window at top left: |
2)
Choose
the method that you prefer for viewing the
results:  The results can be viewed as a summary table tabular format) or as a map graphic. All of the graphics are viewed with the java applet Chromoscape, which is an interactive program that works directly on the user's machine and has a number of features for manipulation and viewing of the graphic. For optimal viewing of graphics, it is strongly recommended that users first read the Chromoscape help sections. |
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3) Select
the method in which you would like to define a
region. Currently,
there are 3 options. The first option is to define
the region
of interest by two flanking markers. For this
option, select "Flanking
markers": In this search, you type in the markers that flank the region of interest in the text boxes that appear at the right: markers can be gene symbols, polymorphisms, or anonymous DNA markers. |
| The
other two search options are based upon
cytogenetic positions.
The cytogenetic
search option allows a user to select a region of a chromosome that
is specified by two flanking In this case, pop-up windows displaying appropriate cytogenetic bands for the selected chromosome appear at right, as shown above. You would select one cytogenetic band from the first popup menu and a second band from the second menu. |
cytogenetic
positions, by selecting "Cytogenetic position":| The
final cytogenetic search option allows you to search by clickable
ideogram. This can be performed simply by clicking on a given chromosome
band displayed in an ideogram of the selected chromosome. The corresponding chromosome ideogram then appears on the right side of the page, as shown in the figure. Each chromosomal band can then be selected simply by clicking upon the cytogenetic band in the chromosome ideogram.
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First,
select "Clickable ideogram" as shown:An
additional checkbox allows the user to include genomic elements that
have been poorly localized in the results.
Poorly localized elements include those with poor support for localization
to a chromosome, and those whose mapping interval is substantially
large.
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4) At bottom right, there should be a submit button visible. Click this button to start the search. For the clickable ideogram option, no submit button is present because clicking on a band commences the search. |
