Table 1 List of covariates included in the model and method/algorithm of calculation.
From: A multivariate prediction model for microarray cross-hybridization
Covariate | Description | Method |
|---|---|---|
X1 | Probe sequence length | count |
X2 | Probe GC content (%) | count |
X3 | Target length | count |
X4 | Target GC content (%) | count |
X5 | Smith-Waterman score | alignment (SW*) |
X6 | E-value | alignment (SW*) |
X7 | Percent identity | alignment (SW*) |
X8 | Overlap length (base pair) | alignment (SW*) |
X9 | Free energy for probe DNA folding** | Mfold [52] |
X10 | Standardized Euclidian distance | [55] |
X11 | Most contiguous base pairs | customized method |
X12 | GC content of the most contiguous segment | count |