Go to a location on a sequence

To go to a numerical position or select a range on the sequence:

1. Choose Edit > Go To Position or use the keyboard shortcut Ctrl/Cmd+J.

2. Type the desired position or range into the box in the dialog. To specify a range, type in the left coordinate, then two periods (..), then the right coordinate. For example, to include the range from 35-141, type 35..141 into the text box. The “hint” uses number symbols (#) to show the format for entering a range. However, when you enter the range, you must substitute an integer for each number symbol.

Inclusive ranges for the forward strand are typed with the symbol > or < or .. (two dots) between the two positions (e.g., 2500 > 3000). Regardless of the symbol used, sequence selection is always on the forward strand.

3. Click OK.

SeqBuilder Pro positions the cursor at the specified numerical position or selects (highlights) the specified range. If you enter a number that is outside the range of the sequence, you will receive the message “Error: out of bounds.”

To search for a text string in a sequence:

1. Choose Edit > Find or the keyboard shortcut Ctrl/Cmd+F.

You can use this dialog to locate a sequence string (including sequence from a primer), an ORF, a restriction site, or the text for any qualifier field in a feature.

2. Specify one of the following search options:

• • Literal or Allow Ambiguity (DNA or protein) searches for a string like GCTTTAG of up to 256 characters in length. Enter the search string into the text box. When using Literal, searching for the string ACNC will only find the exact match, ACNC. When using Allow Ambiguity searching for the string ACNC will find ACTC, ACCC, ACGC, ACAC, or any other ambiguous base.

*If you selected Allow Ambiguity, one or more X’s added before the search term act as wildcards for an equal number of bases. One or more X’s added after the search term act as wildcards for an equal number of bases minus one. (e.g. XXGAT will return 5-base matches; GATXX will return 4-base matches).

*When performing an ambiguous search with an ‘N’ on the 3’ end of the search query, searches will find matches, but the match selection will not include the base corresponding to the 3’ N in the search. Example: An ambiguous search for NGCN will find NGCNs located anywhere on the sequence, but only the part of the match corresponding to NGC will be selected.

• • ORF (DNA only) searches for open reading frames based on the ORF criteria.
    
    
  • Restriction Site (DNA only) searches for a restriction site. When selected, the Select Enzyme dialog will appear. Choose a site to search for, and then click Done to return to the Find in Sequence dialog.
    
    
  • Feature List searches the qualifier fields for all features in the Features view for the specified search string. This option also applies to primer searches.

3. Choose the strand to search using the Strand options, which are only enabled for nucleotide sequences. Choices are normally Forward, Reverse, or Either strand. When using ORF, you may search either the Forward or Reverse strand.

4. Click Find Next to search right or Find Previous to search left.

Once the Find in Sequence dialog is closed, select Edit > Find Again or use the keyboard shortcut Ctrl/Cmd+G to continue the search based on the last criteria entered.