You can scan a nucleic acid or protein sequence for known consensus sequences and protein sequences for known motifs that are defined in a subsequence file. A subsequence may consist of one, two or three parts, with the permitted gap between each part defined, as well as the allowed mismatch for each part in a search.
- Make the required Sequence window active.
- Choose Analyze | Protein Subsequence.
- Select the Subsequence File button to choose the subsequence file that will be used for the analysis.
- A file selection dialog box is displayed, enabling you to choose the file.
- Choose the required file from the scrolling list and select Choose.
- You can restrict the search to a certain region of the sequence by typing in the base numbers that bracket the region in the Region panel, or by selecting a region from the features table drop-down menu at the right of the text boxes.
- Select your search criteria by choosing from the Search Using drop-down menu as follows:
- - choose all subsequences to use all the subsequences in the selected subsequence file
- - choose selected subsequences to use only the subsequences that you have selected in the subsequence file.
- Select OK to perform the analysis.
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Protein subsequence
