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] |