Locate genomic intervals using Interval Finder

When performing an HD probe search or SNP probe search, or creating probes using Genomic Tiling, you can enter a genomic interval as a parameter. To help you identify genomic intervals of interest, the Interval Finder can produce a list of genomic intervals that are associated with specific annotations.

Note: Interval Finder is not available in the Expression application type.

To use Interval Finder from the CGH, ChIP, or SureSelect Capture Array application types:

Click the Workspace tab. (Interval Finder searches are not available in collaborations.)
Click Probe , then select Interval Finder.

The Interval Finder pane appears.
In Search Type, select one of the following options, then enter the desired search terms as described below.

Option	Instructions/Details
All	This type of search returns intervals that have any annotation that matches a single search term that you enter. In Search Term(s), type the desired term. By default, eArray returns intervals that contain the search term within any associated annotation. To limit returned intervals to those whose annotation matches the search term exactly, mark Exact Search.
Accessions	In Search Term(s), type an accession number, without its source, or multiple accession numbers separated by pipe "\|" characters. The search returns the genomic intervals that correspond with each of the accessions. For the search to return intervals, accessions must match exactly. Use upper case (capital) letters in accessions. Example: NM_012257\|Q0055\|NM_012298 You can also upload a file of accessions. Prepare a plain text file with an extension of .txt. Put one accession on each line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.
Cytoband	In Search Term(s), type a cytoband designation, without its source, or multiple cytobands separated by pipe "\|" characters. The search returns the genomic intervals that correspond with each of the cytobands. For the search to return intervals, cytobands must match exactly. Use lower case letters to specify the p or q chromosome arms. Example: 1p22.2\|2q33.3 You can also upload a file of cytobands. Prepare a plain text file with an extension of .txt. List one cytoband per line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.
Gene Symbol	In Search Term(s), type a gene symbol, or multiple gene symbols separated by pipe "\|" characters. The search returns the genomic intervals that correspond with each of the gene symbols. For the search to return intervals, gene symbols must match exactly. Use upper case (capital) letters in gene symbols. Example: H3N2\|BRMS1\|BRCA1 You can also upload a file of gene symbols. Prepare a plain text file with an extension of .txt. List one gene symbol per line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.

In Species, select the desired species. H. sapiens is selected by default.
Click Search.

eArray retrieves the genomic intervals. A Search Results pane appears. For each interval, the pane shows the associated annotation, the genomic coordinates of the interval, and a brief description.

After eArray displays the retrieved genomic intervals, you can take action on them.

Use the tasks in the table below to navigate among the returned intervals and select them for further action.

Task	Instructions/Details
Select a single interval	Mark the check box in its row.
Select additional intervals	Mark the check boxes next to the name of each desired interval. eArray remembers your selections if you navigate to different pages.
Go to another page of Search Results	Click the Pages links. eArray remembers your selections as you go from page to page.
Sort the results	Click the heading of a column. eArray sorts the results based on the contents of the given column. To reverse the order of the items in the list, click the heading again.
Select all intervals on all pages	Mark Select Entire Result.
Select all intervals on one page	Mark the check box in the column heading row.

Use the tasks in the table below to take action on the intervals that you selected in the previous step.

Task	Instructions/Details
Download the selected intervals as a list	Click Download. A progress message appears, and a File Download dialog box opens. Click Save. A Save As dialog box appears. Select a location for the downloaded file, then click Save. eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one interval on each line.
Download the selected intervals as a BED format file	This task can be useful if you want to use the selected intervals in a genome browser or other software that accepts BED format files. Click Download in BED Format. A progress message appears, and a File Download dialog box opens. Click Save. A Save As dialog box appears. Select a location for the downloaded file, then click Save. eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one interval on each line. The file contains only the genomic coordinates of the selected intervals.
Start a new HD search based on the selected intervals	(CGH and ChIP application types) Click Run HD Search. The Standard Genomic Intervals HD Search page appears. The selected intervals appear in pipe-separated format in Genomic Intervals. Set the other search parameters, as needed, then click Search. See To do a Standard Genomic Intervals HD Search.
Start a Genomic Tiling job based on the selected intervals	(SureSelect Capture Array application type) Click Run Genomic Tiling. The Genomic Tiling page appears. The selected intervals appear in pipe-separated format in Genomic Intervals. Set the other Genomic Tiling parameters, as needed, then click Submit. See Set up a Genomic Tiling job. Note: To use retrieved intervals for a Genomic Tiling job in the CGH and ChIP application types, download the intervals. When you set up the Genomic Tiling job, upload them in the Genomic Intervals tiling parameter.
Start a SNP probe search based on the selected intervals	(CGH application type) Download the selected intervals, as described at the top of this table, then upload them in the Genomic Intervals parameter. See Search for SNP probes.
Download a list of the search terms that did not return any intervals	Click Download Unfound Terms. A progress message appears, and a File Download dialog box opens. Click Save. A Save As dialog box appears. Select a location for the downloaded file, then click Save. eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one unfound term on each line.
View a list of the chromosomes associated with the selected intervals	Click List Chromosomes. A list of the chromosomes represented in the selected intervals appears in a new window.