User GuidesSnapGene User Guide SearchingSearch for Similar DNA Sequences

Search for Similar DNA Sequences

How do I search for DNA sequences while allowing for mismatches and gaps or insertions?

"Find Similar DNA Sequences"  is available in SnapGene 5.2 and later.

Show the Find Controls

To show the Find controls in a DNA sequence file, click Edit Find Find Similar DNA Sequences.  

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

Enter the Query DNA Sequence


  • In a search for similar DNA sequences, the minimum query length depends on the number of allowed mismatches. By default, the minimum query length is 10 bases.
  • The query cannot be enclosed by quotes.

Enter the query DNA sequence in the search box.

Use the drop-down menus to set whether to allow a "mismatch or gap/insertion" or a "mismatch only", and to specify the allowed frequency.

Use the Next and Previous buttons to jump between similar sequence matches.

Search with Ambiguous Bases

To allow ambiguities at a specific position in the query sequence, use a degenerate DNA letter code such as W (A or T) at that position.

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, !T means not T.

Alternatively, enclose the excluded bases in parentheses. For example, !(TA) means not T, A, or W.  

Review Recent Searches

To review or reuse recent searches, click the arrow button at the end of 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 match will be highlighted in yellow, and the query will be displayed next to the match with any differences marked in red. 

Show the Search Tips

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

Alternatively, choose Search Tips from the Find controls.