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Table 5 Different types of string kernels (see Table 1 for further details)

From: Encodings and models for antimicrobial peptide classification for multi-resistant pathogens

Encoding Description Summary Used in Used along with
Spectrum Kernel generates all possible subsequences of length k and counts the occurrences of these k-mers Density: -
Information: -
[112]  
Mismatch Kernel considers a certain distance, hence mismatches, between two k-mers Density: -
Information: o
[114,115,116] General Structure
Distant Segment Kernel allows a gap between two k-mers Density: -
Information: o
[118]  
Local Alignment Kernel obtained from local alignment scores Density: +
Information: o
[119] Spectrum Kernel, Mismatch Subsequence Kernel
Subsequence Kernel measures sequence similarity, gaps within k-mers are taken into account Density: +
Information: o
[119] Frequency of Amino Acid Pairs
Frequency of Amino Acid Pairs similar to dipeptide composition Density: -
Information: o
[119]  
String Kernels + Physicochemical Properties optimization of existing string kernels such that these involve physicochemical properties Density: +
Information: +
[120] Physicochemical Properties
Generic String Kernel string kernel with physicochemical properties and penalization of non adjacent segments Density: +
Information: +
[121, 122]