Table 1 Descriptions of the motif optimization algorithms evaluated
From: Comparison of discriminative motif optimization using matrix and DNA shape-based models
Algorithm | Output | Description |
|---|---|---|
JASPAR | Position frequency matrix | PFMs from the JASPAR database |
DAMO | Position weight matrix | Modified DiMO program that outputs PWMs instead of PFMs |
DAMO_PFM | Position frequency matrix | PFMs derived from the DAMO single-nucleotide PWMs |
DAMO_dinuc | Position weight matrix | The adjacent di-nucleotide mode of DAMO |
DNAshapedTFBS_4bit | Gradient boosting classifier | DNAshapedTFBS with 4-bit encoding |
DNAshapedTFBS_4bit + shape | Gradient boosting classifier | DNAshapedTFBS_4bit plus DNA shape features |
Shape_only | Gradient boosting classifier | The feature vector contains only DNA shape features |
JASPAR + shape | Gradient boosting classifier | JASPAR PFM score plus DNA shape features |
DAMO + shape | Gradient boosting classifier | DAMO single-nucleotide PWM score plus DNA shape features |