Search for a Translated Protein Sequence in a DNA Sequence

Open the DNA file to search.

To show or hide the Find controls, click the Find button in the bottom left corner of Map or Sequence view, then choose "Find protein sequence:" via the drop down menu.

Alternatively, click menu Edit → Find → Find Similar Protein Sequence.

If you also wish to search for a protein translation regardless of location, toggle on the Show Translations button and choose a specific reading "Frame" or a combination of reading "Frames".

1. Enter the amino acid sequence you wish to search for in the search field, then click Next.  
2. If one or more matches are found then the number will be reported in the bar.
3. Use the Previous/Next buttons to step between multiple matches.
4. Matches will be highlighted on the Map or Sequence view. See more details below.
5. Information about the current selected "match" is shown in the bottom bar.

To allow any amino acids at a specific position, use X.

To exclude amino acids at a particular position, use an exclamation point in front of the forbidden amino acids. For example, !P means not P.

Alternatively, enclose the excluded amino acids in parentheses. For example, !(ST) means not S or T.

To search for a degenerate amino acid, enclose the entire query in quotes. For example, a search for X will find all matches to any letter (A-Z), but a search for "X" will find only bases actually represented as X.

The other degenerate amino acids are B (matching either D or N) and Z (matching either E or Q).

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

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

In Sequence view, the corresponding nucleotide sequence will be selected, and the matching protein sequence will be highlighted in blue.

To view examples of protein searches, click Help → Search Tips, then scroll down.

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