Locate genomic intervals using Interval Finder

 

When creating probes using Bait 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.

To use Interval Finder from the SureSelect Target Enrichment and SureSelect RNA Enrichment application types:

  1. Click the Workspace tab. (Interval Finder searches are not available in collaborations.)

  2. Click Baits, then select Interval Finder.

    The Interval Finder pane appears.

  3. 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.

  1. In Search Term(s), type the desired term.

  2. 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.

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

  2. 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.

  1. 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.

  1. 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

  1. Click Download.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. 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.

  1. Click Download in BED Format.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. 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 Bait Tiling job based on the selected intervals

(SureSelect Target Enrichment and SureSelect RNA Enrichment application types)

  1. Click Run Bait Tiling.
    The Bait Tiling page appears. The selected intervals appear in pipe-separated format in Genomic Target Intervals.

  2. Set the other Bait Tiling parameters, as needed, then click Submit. See Bait Tiling (SureSelect Target Enrichment) and Bait Tiling (SureSelect RNA Enrichment).

Download a list of the search terms that did not return any intervals

  1. Click Download Unfound Terms.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. 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.

See also

Locate exon intervals using Exon Interval Finder