Concept
To avoid completely losing the sequence-order information, the concept of PseAA (pseudo amino acid) composition was proposed. In contrast with the conventional amino acid composition that contains 20 components with each reflecting the occurrence frequency for one of the 20 native amino acids in a protein, the PseAA composition contains a set of greater than 20 discrete factors, where the first 20 represent the components of its conventional AA composition while the additional factors incorporate some sequence-order information via various modes.
The additional factors are a series of rank-different correlation factors along a protein chain, but they can also be any combinations of other factors so long as they can reflect some sorts of sequence-order effects one way or the other. Therefore, the essence of PseAA composition is that on one hand it covers the AA composition, but on the other hand it contains the information beyond the AA composition and hence can better reflect the feature of a protein sequence through a discrete model.
Meanwhile, various modes to formulate the PseAA composition have also been developed, as summarized in a review.
Read more about this topic: Pseudo Amino Acid Composition
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