Showing posts from May, 2014

Hydrophobicity Plot using BioPython

Hydrophobicity is the property of being water repellent, tending to repel and not absorb water. Calculation of hydrophobicity in proteins is important in identifying its various features. This can be membrane spanning regions, antigenic sites, exposed loops or buried residues. Usually, these calculations are shown as a plot along the protein sequence, making it easy to identify the location of potential protein features. The hydrophobicity is calculated by sliding a fixed size window (of an odd number) over the protein sequence. At the central position of the window, the average hydrophobicity of the entire windows is plotted. A hydrophobicity plot is a quantitative analysis of the degree of hydrophobicity of amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein. The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity on its y-axis. In hydrophobicity plot, the degree of hydrophobicity is tak