Importing, Viewing, and Exploring a Protein Sequence Using a Graphical Interface

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Overview of the Sequence Tool Viewing Amino Acid Sequence Statistics Closing the Sequence Tool References

Overview of the Sequence Tool

The Sequence Tool window integrates many of the sequence functions in the toolbox. Instead of entering commands in the MATLAB Command Window, you can select and enter options.

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Viewing Amino Acid Sequence Statistics

The following procedure illustrates how to view an amino acid sequence for an ORF located in a nucleotide sequence. You can import your own amino acid sequence, or you can get a protein sequence from the GenBank database. This example uses the GenBank accession number NP_000511.1, which is the alpha subunit for a human enzyme associated with Tay-Sachs disease.

1. Select File > Download Sequence from > NCBI.

   The Download Sequence from NCBI dialog box opens.

2. In the Enter Sequence box, type an accession number for an NCBI database entry, for example, NP_000511.1. Click the Protein option button, and then click OK.

   

   The MATLAB software accesses the NCBI database on the Web and loads amino acid sequence information for the accession number you entered.

   

3. Select Display > Amino Acid Color Scheme, and then select Charge, Function, Hydrophobicity, Structure, or Taylor. For example, select Function.

   The display colors change to highlight charge information about the amino acid residues. The following table shows color legends for the amino acid color schemes.

   

Amino Acid Color Scheme	Color Legend
Charge	Acidic — Red Basic — Light Blue Neutral — Black
Function	Acidic — Red Basic — Light Blue Hydropobic, nonpolar — Black Polar, uncharged — Green
Hydrophobicity	Hydrophilic — Light Blue Hydrophobic — Black
Structure	Ambivalent — Dark Green External — Light Blue Internal — Orange
Taylor	Each amino acid is assigned its own color, based on the colors proposed by W.R. Taylor.

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Closing the Sequence Tool

Close the Sequence Tool window from the MATLAB command line using the following syntax:

seqtool('close')

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References

[1] Taylor, W.R. (1997). Residual colours: a proposal for aminochromography. Protein Engineering 10, 7, 743–746.

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Importing, Viewing, and Exploring a Nucleotide Sequence Using a Graphical Interface

Example: Sequence Alignment

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