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Explore a Protein Sequence Using the Sequence Viewer App

Overview of the Sequence Viewer

TheSequence Viewerapp integrates many of the sequence functions in the Bioinformatics Toolbox™ toolbox. Instead of entering commands in the MATLAB®Command Window, you can select and enter options using the app.

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, which is the alpha subunit for a human enzyme associated with Tay-Sachs disease.

  1. SelectFile > Download Sequence from > NCBI.

    The从NCBI下载序列dialog box opens.

  2. In the dialog box, type an accession number for an NCBI database entry, for example,NP_000511. Click theProteinoption button, and then clickOK.

    TheSequence Vieweraccesses the NCBI database on the Web and loads amino acid sequence information for the accession number you entered.

  3. SelectDisplay > Amino Acid Color Scheme, and then selectCharge,Function,Hydrophobicity,Structure, orTaylor. For example, selectFunction.

    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 byW.R. Taylor.

Closing the Sequence Viewer

Close theSequence Viewerfrom the MATLAB command line using the following syntax:

seqviewer('close')

References

[1] Taylor, W.R. (1997). Residual colours: a proposal for aminochromography. Protein Engineering10, 7, 743–746.