I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil".

analysed_seq = ProteinAnalysis("AKVLGSLEALEPVHYEEKNWCE")
analysed_seq.protein_scale(Scale, WindowSize, Edge)

Known parameters

  • WindowSize refers to the total number of amino acids to be considered either side of the residue (an int variable).
  • Edge refers to the weighting of the scale further from the centre of the window (0-1). `

Unknown parameter

  • Scalerefers to which scale being used. I am interested in how to give theScale` variable a valid variable.

The Biopython docs simply point out that there are many scales to choose from and the source code doesn't seem to give any clues about scale options.

Where can I find a list of the scale are available and how to call them?


Use this line of code:

print(analysed_seq.protein_scale(analysed_seq.get_amino_acids_percent(), window=9, edge=0.4))
  • 1
    $\begingroup$ Welcome to the forum. Can you add some context as to what this line is doing and why it answers the question? $\endgroup$
    – Bioathlete
    Jan 6 '20 at 14:49

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