User GuidesSnapGene User Guide SearchingSearch for an Exact DNA Sequence

Search for an Exact DNA Sequence

How do I search for a DNA sequence?

Show the Find Controls

To show the Find controls, click Edit Find Find DNA Sequence.  

The Find controls will appear near the bottom of the window.

Enter the DNA Sequence

Enter the DNA sequence you wish to search for in the search box, then click Next.  If a match is found it will be highlighted on the sequence or map view, as described below. 

Search with Ambiguous Bases

To allow multiple bases at a specific position in the query sequence, use parentheses to enclose the set of allowed bases.

In the example shown in the screenshot, either A or G will be allowed at the designated position. SnapGene will find matches to either GGTCTACTTC or GGTCTGCTTC.

Alternatively, to allow multiple bases at a position, use a degenerate DNA letter code such as R.

To view a list of DNA letter codes, click Tools → Letter Codes.

Search with Excluded Bases

To exclude bases at a particular position, use an exclamation point in front of the forbidden bases. For example, !R means not A, G, or R.

Alternatively, enclose the excluded bases in parentheses. For example, !(AG) means not A, G, or R.  

Search for a Degenerate Base

To search for a degenerate base, enclose the query in quotes. For example, a search for R will find all matches to A or G or R, but a search for "R" will find only bases that are actually represented as R.

Review Recent Searches

To review or reuse recent searches, click the arrow button on the search box.

See the Matches in Map View

In Map view, a matching DNA sequence will be highlighted in blue.

See the Matches in Sequence View

In Sequence view, a matching DNA sequence on either strand will be highlighted in green.

Show the Search Tips

To view examples of DNA searches, click Help → Search Tips.

Alternatively, choose Search Tips from the Find controls.