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Pairs of k-spaced amino acids

SA Sabit Ahmed
AR Afrida Rahman
MH Md. Al Mehedi Hasan
SA Shamim Ahmad
SS S. M. Shovan
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The formation of k-spaced amino acid pairs encoding technique12,21,35 calculates the occurrence frequencies of the pairs of k-spaced amino acids from a segmented protein sample, that can express the short linear motif information out of it12,30. For instance, the encoding of a peptide segment will be a 441-dimensional feature vector if k=0. This can be defined as,

where n stands for any of amino acid, NTotal means the occurrence frequency of all k-spaced amino acid pairs35 and NAnA means the occurrence frequency of the AnA pairs in the segment20 when k=0. In this study, after merging each of the 441-dimension feature vectors for k=0,1,2,3,4, a total of 2205-dimensional features have been formed.

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