Searching within the Sequence Viewer

• Sequence Coordinate Searches
• Search for SNP
• Search for Gene
• Search for Component
• Search Sequence
• Track Search

When Sequence Viewer is embedded on a web page, or in the stand-alone Sequence Viewer application, searches can be initiated from the “Find:” box on the top toolbar (below, left) or by selecting “Search” in the Tools menu (below, right).

For information on searching within NCBI genome browsers, such as the Genome Data Viewer (GDV), please see the corresponding Help documentation.

The following terms can be used to search sequence displays:

• Sequence coordinates
• Reference SNP IDs and HGVS expressions (see demo examples)
• Gene symbols
• INSDC nucleotide/protein accessions annotated on the sequence
• IUPAC sequence strings
• Keywords found in track names and descriptions

Searches are initiated by pressing the Enter key. Successful searches will either update the display or show results in one of the horizontal tabs in the Search Results dialog .

Sequence Coordinate Searches

The Sequence Viewer search function can be used to locate a specific position or range. Examples of supported coordinate syntaxes include:

• 100
• 5-515
• 5..515
• 5 to 515
• 10k-20k
• 1m-2m

When a specific coordinate position is entered in the search box, the viewer re-centers at this position at the current zoom level and a marker is automatically added at the coordinate.

When a coordinate range is entered in the search box, the visible range in the viewer is changed to the specified range. The insets in the image below show that the ends of the visible range correspond to the range in the “Find:” box.

Search for SNP

For human sequences, the Sequence Viewer search function can be used to search for reference SNPs (e.g. rs4970989) from the NCBI SNP database. If the SNP is found in the assembly/molecule, the view moves to the vicinity of the SNP and a marker is automatically added at the SNP position.

Search for Gene

You can search for a gene using the gene symbol or full gene name. Results for gene searches appear in the Features tab of the Search Results table. Double-clicking on a search result re-centers the viewer around the gene.

Search for Component

You can search for contigs or scaffolds that are components of a larger sequence by their accessions. Search results appear in the Components tab of the Search Results table. Double-clicking on a search result re-centers the viewer around the coordinates reported in the table.

Search Sequence

Sequences can be searched using IUPAC nomenclature for nucleic acids or proteins. Regular expressions are supported, e.g. “atg{5}” to find atggggg. Search results appear in the Sequence tab of the Search Results table. Double-clicking on a search result zooms to the sequence match, which is highlighted.

Track Search

The Sequence Viewer search function can also be used to find and add data tracks to the viewer using a keyword in the track name. Only tracks that have been made available to the particular instance of the graphical sequence viewer are in scope for this search. The complete list of available tracks can be found in the track configuration panel.

Search results appear in the Tracks tab of the Search Results table. A track can be added to the viewer by selecting the check box and clicking the button to “Re-configure”.