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FEBS Lett. 1987 Nov 16;224(1):149-55.

Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences.

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Groupe Cristallographie et Simulations Interactives des Macromolécules Biologiques, CNRS UA09, Université, Paris, France.


A new method for comparing and aligning protein sequences is described. This method, hydrophobic cluster analysis (HCA), relies upon a two-dimensional (2D) representation of the sequences. Hydrophobic clusters are determined in this 2D pattern and then used for the sequence comparisons. The method does not require powerful computer resources and can deal with distantly related proteins, even if no 3D data are available. This is illustrated in the present report by a comparison of human haemoglobin with leghaemoglobin, a comparison of the two domains of liver rhodanese (thiosulphate sulphurtransferase) and a comparison of plastocyanin and azurin.

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