Find exon intervals

The Exon Interval Finder returns a list of the exonic genomic intervals that are associated with specific genomic targets. In a Simple Search, you can specify a single search string, and the program returns all exonic intervals whose annotation contains that search string. In an Advanced Search, you can specify multiple values for specific types of annotations, and the program returns the intervals whose annotation exactly matches your search terms. The Exon Interval Finder is available for the SureSelect Target Enrichment application type.

From the search results, you can select exonic intervals of interest and use them as input intervals for a Bait Tiling job, and you can also download the intervals, and view a list of chromosomes that are associated with them.

Note: eArray can also find genomic intervals of interest without regard to their exon content. See How to use Interval Finder.

This help topic has the following sections:

Exon Interval Finder (Simple Search) – In this search method, you type a search string, and the program returns exonic genomic intervals that contain the search string in any of their annotation.
Exon Interval Finder (Advanced Search) – In this search method, you specify one or more accession numbers, cytobands, and/or gene symbols. The program returns exonic genomic intervals that match any of the values.
Take action on the results of an Exon Interval Finder search

Exon Interval Finder (Simple Search)

Set the application type to SureSelect Target Enrichment.
Click the Workspace tab or enter a collaboration.
Click Baits, then select Exon Interval Finder.

A search pane appears.
Specify the following search criteria. Both are required.
- Search Term – Type a search term in the box. The program returns the locations of all exons whose annotation contains this term. The search term is not case-sensitive.
- Species – Select the desired species from the list. To select all available species, select All.
Click Search.

A search results pane displays the annotation(s) that contain your search term, and the exonic intervals that are associated with the annotations. The results also indicate whether the exon is found on the + strand or the – strand of the DNA. For annotations that are associated with multiple exons, eArray lists each exon on a separate line. You can take action on the intervals in the search results. See Take action on the results of an Exon Interval Finder search, below.

Exon Interval Finder (Advanced Search)

Set the application type to SureSelect Target Enrichment.
Click the Workspace tab or enter a collaboration.
Click Baits, then select Exon Interval Finder.

The Interval Finder pane appears.
At the bottom of the pane, click Advanced Search.

The Advanced Search pane of the Exon Interval Finder appears.
Specify one or more of the following search criteria. eArray returns exonic intervals that match any of the search terms exactly.

Criterion	Instructions/Details
Accessions	Type an accession number, without its source, or multiple accession numbers separated by pipe "\|" characters. The search returns the exonic 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. List one accession 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.
Cytoband	Type a cytoband designation, without its source, or multiple cytobands separated by pipe "\|" characters. The search returns the exonic 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	Type a gene symbol, or multiple gene symbols separated by pipe "\|" characters. The search returns the exonic 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.
Species	Select a species from the list. This restricts your search to exonic intervals that are associated with the selected species. To return relevant intervals for all available species, select All.

Click Search.

A search results pane displays the annotation(s) that you provided as search terms, and the exonic intervals that are associated with them. The results also indicate whether the exon is found on the + strand or the – strand of the DNA. For annotations that are associated with multiple exons, eArray lists each exon on a separate line. You can take action on the intervals in the search results. See Take action on the results of an Exon Interval Finder search, below.

Take action on the results of an Exon Interval Finder search

After eArray displays the retrieved exonic intervals, you can download them, use them as the basis of a Bait Tiling job, and view the list of chromosomes represented by them.

To navigate among the intervals in the Search Results, and to select them for further action, do any of the following:

Task	Instructions/Details
Select a single interval	Mark the check box in its row.
Select additional intervals	Mark their check boxes. eArray remembers your selections if you navigate to different pages.
Go to another page of Search Results	Click the Pages links.
Sort the results	Click the heading of a column. eArray sorts the results based on the content of the column that you click. To reverse the order of the sort, 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.

Do any of the following:

Task	Instructions/Details
Download the selected intervals	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 exonic intervals in ZIP format. The ZIP archive contains a single .tdt file with the intervals listed one per line. Note:* If you have difficulty downloading the file, hold down the Control ( Ctrl) key as you do the first two steps of this procedure. This bypasses pop-up blocking software.
Start a Bait Tiling job based on the selected intervals.	Click Run Bait Tiling. The Bait Tiling page appears. The selected exonic intervals appear in pipe-separated format in Genomic Target Intervals. Set the other Bait Tiling parameters, as needed, then click Submit. See Bait Tiling.
View a list of the chromosomes associated with the selected intervals	Click List Chromosome. A list of the distinct chromosomes represented by the selected exonic intervals appears in a new window.