Hydrophobicity Grapher How-to Information

Submitting files for graphing

Graph a user-supplied sequence
Graph protein sequence(s) from the VOCS database

Working with the Hydrophobicity Plot

Zooming in and out
Changing graphing parameters
Deleting unwanted sequences


Graph a user-supplied sequence

Hydrophobicity Plotter is capable of graphing amino acid sequences in three formats:

  • Plain text sequences
  • Fasta files
  • Genbank files

To graph a sequence in text form, select “Paste in an amino acid sequence” from the File menu. Paste the sequence into the box that appears, in text format (i.e. a single string of single-letter amino acid abbreviations with no whitespace, special characters, or headers.) Click “Make the Plot” and the graph will automatically appear.

To load a FASTA or Genbank file, select “Load amino acid sequence(s) from FASTA/Genbnk file” from the File menu. Find the file on your computer and click “Load.” Note that each file you load must contain only a single sequence; FASTA files with multiple headers and sequences will not be processed correctly! To graph multiple sequences, repeat  the loading step for each sequence.


Graph protein sequence(s) from the VOCS database 

At the moment, Hydrophobicity Grapher is not set up to directly access the VOCS databases. However, Hydrophobicity Grapher can be launched from within VOCS. If you wish to graph one or more protein sequences from the VOCS database, begin by opening VOCS. Perform a search for the genes of choice, than, from the Tools menu, select “Hydrophobicity Plot.” Hydrophobicity Grapher will automatically open with a graph of the selected proteins.


Zooming in and out

To zoom into a region of interest within the plot, click and drag the mouse arrow to select the region. The plot will automatically resize to zoom into the selected area. The Amino Acid Count on the X-axis tells you what part of the sequence you are looking at.

To zoom back to the original graph size, click the Reset View button below the graph, or select “Reset” from the View menu.


Changing graphing parameters

Hydrophobicity Grapher offers two graphing parameters that you can adjust:

  • Hydrophobicity Scale System: Kyte-Doolittle, Hopp-Woods, or Parker-Guo-Hodges.
  • Window size can be freely varied by the user. Each point on the graph is calculated using the hydrophobicity average of the neighboring amino acids; window size determines how many neighboring residues are used in this operation. A larger window size will give a smoother graph, while a smaller one will give a more detailed graph.

Both window size and hydrophobicity scale can be adjusted using the options directly above the graph. Alter the parameters as wished and click Replot.


Deleting unwanted sequences

To delete one or more unwanted sequences from the plot while leaving others in place, select “Select Sequences to Delete” from the File menu. A list of currently plotted sequences will open; select one or more (hold down the CTRL key to select multiple sequences), then click OK.

To remove all sequences from the plot, click the Clear Window button below the graph.


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