Sequence Analysis and Alignment

In this example, you are interested in generating a web form graphical user interface that will display statistics for a nucleotide sequence and align it with another sequence. The window below displays the equivalent MATLAB commands that, when entered into the MATLAB Command Window, would produce the same results as the button events on this form.

Note that this example must be run in a browser that supports VBScript. Also, the browser's security settings must be set to enable ActiveX controls to run in scripts. For example, in Internet Explorer, go to Tools->Internet Options->Security and select "Custom Level." The "Initialize and script ActiveX controls not marked as safe" setting must be set to either Enable or Prompt.

Clear history:

MATLAB can retrieve the data for a nucleotide sequence given an NCBI number. To search for an NCBI number, go to the National Center for Biotechnology Information website. Then select "Nucleotide" from the Search menu and enter the sequence of interest. The default values included below are the result of searching for the enzyme hexosaminidase A in humans and mice.

After entering new numbers and names for the desired nucleotide sequences, or keeping the default values as an example, you can proceed to show a count of nucleotides. First select which of the sequences you would like to view and then select the nucleotide category. The "Show Count" button will display a count of each of the nucleotide types in the text window. The "Visualize" button will display a graphical representation of the nucleotide count in a new figure window. You can then display the Open Reading Frames of the sequences, and finally, align particular frames. You can either globally align the sequence frames or use the Smith-Waterman algorithm for a local alignment.

1. Select first and second sequences.


Enter first sequence number:

Enter first sequence name:

Enter second sequence number:

Enter second sequence name:

Load sequences:


2. Show statistics for sequences.


Select loaded sequence:

Select type of nucleotide to count:

Show nucleotide count:

Display graphical representation of count:

Display Open Reading Frames:


3. Align the first sequence with the second sequence:


Select frame number for first sequence:

Select frame number for second sequence:

Execute global alignment:

Execute local alignment:

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